From 223cb32a45a3b29170a51a60242961a2012eb7e6 Mon Sep 17 00:00:00 2001 From: Hancheng Zhao Date: Tue, 2 Jan 2024 01:20:30 -0500 Subject: [PATCH 1/9] mpi debug --- spatial_decompose/MDargon_spatial.py | 78 ++++++++++++++++++++-------- spatial_decompose/job.err | 45 ---------------- spatial_decompose/job.out | 21 ++------ spatial_decompose/job.sh | 4 +- 4 files changed, 60 insertions(+), 88 deletions(-) diff --git a/spatial_decompose/MDargon_spatial.py b/spatial_decompose/MDargon_spatial.py index 936447d..10f1937 100644 --- a/spatial_decompose/MDargon_spatial.py +++ b/spatial_decompose/MDargon_spatial.py @@ -5,11 +5,7 @@ import utils_spatial_decompose as ut from mpi4py import MPI -comm = MPI.COMM_WORLD -rank = comm.Get_rank() -size = comm.Get_size() -print('initial rank', rank) - +# run params stop_step=1 k_B=1.38064852*10**(-23) dt=0.002 @@ -29,25 +25,61 @@ part_type='LJ' name='argon256' +comm = MPI.COMM_WORLD +rank = comm.Get_rank() +size = comm.Get_size() +print(rank,size) +comm.barrier() + if rank==0: - start_time=time.time() - print(rank, start_time) -comm.barrier() -info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, - position_init=position_init, - dt=dt, - stop_step=stop_step, - accel_init=a_init, - r_cut=2.8, - L=L0, - T_eq=T_equal, - e_scale=energy_scale, - sig=sigma) -if rank == 0: - end_time=time.time() - period = end_time-start_time - print("For this {} steps operation (dt={}) with r_cut = {} and L = {}, it took:".format(stop_step,dt,r_c,L0),end_time-start_time,'s') - ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, 1000, False) + start_time = time.time() + + # # initialize + k_B=1.38064852*10**(-23) + size_sim=position_init.shape[0] + x_dot_init=ut.random_vel_generator(size_sim,T_equal,e_scale) + #initialize PE, KE, T_insta, P_insta, Momentum + PE=np.zeros((stop_step+1,1)) + KE=np.zeros((stop_step+1,1)) + T_insta=np.zeros((stop_step+1,1)) + P_insta=np.zeros((stop_step+1,1)) + #initialize the info matrix + info=np.zeros((stop_step+1,size_sim,9)) + info[0,:,:]=np.concatenate((position_init,x_dot_init,accel_init),axis=1) + infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L) + #zero step value + PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_cut,L=L) + KE[0,:]=ut.Kin_Eng(info[0,:,3:6]) + T_insta[0,:]=2*KE[0,:]*e_scale/(3*(size_sim-1)*k_B) #k + P_insta[0,:]=ut.insta_pressure(L,T_insta[0],info[0,:,0:3],r_cut,e_scale) #unitless +else: + infotodic = None + # info = None +comm.barrier() +infotodic = comm.bcast(infotodic, root = 0) + +if rank == 0: + end_time = time.time() + print(f'Run time is {end_time-start_time:.3f}') +comm.barrier() + + +# if rank==0: +# start_time=time.time() +# info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, +# position_init=position_init, +# dt=dt, +# stop_step=stop_step, +# accel_init=a_init, +# r_cut=2.8, +# L=L0, +# T_eq=T_equal, +# e_scale=energy_scale, +# sig=sigma) +# end_time=time.time() +# period = end_time-start_time +# print("For this {} steps operation (dt={}) with r_cut = {} and L = {}, it took:".format(stop_step,dt,r_c,L0),end_time-start_time,'s') +# ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, 1000, False) # else: # LJ_MD(subdiv=subdiv, # position_init=position_init, diff --git a/spatial_decompose/job.err b/spatial_decompose/job.err index 244518c..44b3128 100644 --- a/spatial_decompose/job.err +++ b/spatial_decompose/job.err @@ -17,48 +17,3 @@ See 'conda init --help' for more information and options. IMPORTANT: You may need to close and restart your shell after running 'conda init'. -------------------------------------------------------------------------------- -There are messages associated with the following module(s): -------------------------------------------------------------------------------- - -cuda/11.1.1: - Warning - This module has been deprecated and is scheduled for removal. - Please transition to a module from the production pool instead. - -------------------------------------------------------------------------------- - -Traceback (most recent call last): - File "/ocean/projects/cts180021p/hzhao3/ParallelComputing/EECS587Project/spatial_decompose/MDargon_spatial.py", line 36, in - info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, - File "/ocean/projects/cts180021p/hzhao3/ParallelComputing/EECS587Project/spatial_decompose/LJ_SpatialDecomp.py", line 41, in LJ_MD - info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) -AttributeError: 'NoneType' object has no attribute 'P' -Traceback (most recent call last): - File "/ocean/projects/cts180021p/hzhao3/ParallelComputing/EECS587Project/spatial_decompose/MDargon_spatial.py", line 36, in - info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, - File "/ocean/projects/cts180021p/hzhao3/ParallelComputing/EECS587Project/spatial_decompose/LJ_SpatialDecomp.py", line 41, in LJ_MD - info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) -AttributeError: 'NoneType' object has no attribute 'P' -Traceback (most recent call last): - File "/ocean/projects/cts180021p/hzhao3/ParallelComputing/EECS587Project/spatial_decompose/MDargon_spatial.py", line 36, in - info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, - File "/ocean/projects/cts180021p/hzhao3/ParallelComputing/EECS587Project/spatial_decompose/LJ_SpatialDecomp.py", line 41, in LJ_MD - info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) -AttributeError: 'NoneType' object has no attribute 'P' -Traceback (most recent call last): - File "/ocean/projects/cts180021p/hzhao3/ParallelComputing/EECS587Project/spatial_decompose/MDargon_spatial.py", line 36, in - info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, - File "/ocean/projects/cts180021p/hzhao3/ParallelComputing/EECS587Project/spatial_decompose/LJ_SpatialDecomp.py", line 41, in LJ_MD - info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) -AttributeError: 'NoneType' object has no attribute 'P' --------------------------------------------------------------------------- -Primary job terminated normally, but 1 process returned -a non-zero exit code. Per user-direction, the job has been aborted. --------------------------------------------------------------------------- --------------------------------------------------------------------------- -mpirun detected that one or more processes exited with non-zero status, thus causing -the job to be terminated. The first process to do so was: - - Process name: [[18937,1],3] - Exit code: 1 --------------------------------------------------------------------------- diff --git a/spatial_decompose/job.out b/spatial_decompose/job.out index 069f2b8..05e9ad6 100644 --- a/spatial_decompose/job.out +++ b/spatial_decompose/job.out @@ -1,18 +1,5 @@ -/opt/packages/openmpi/gcc/4.1.1-gcc8.3.1-cpu/bin/mpiexec -/opt/packages/openmpi/gcc/4.1.1-gcc8.3.1-cpu/bin/mpirun -MPI startup(): PMI server not found. Please set I_MPI_PMI_LIBRARY variable if it is not a singleton case. -MPI startup(): PMI server not found. Please set I_MPI_PMI_LIBRARY variable if it is not a singleton case. -MPI startup(): PMI server not found. Please set I_MPI_PMI_LIBRARY variable if it is not a singleton case. -MPI startup(): PMI server not found. Please set I_MPI_PMI_LIBRARY variable if it is not a singleton case. +/opt/intel/oneapi/intelpython/latest/bin/mpiexec +initial rank 1 +initial rank 3 initial rank 0 -0 1704156354.2576318 -initial rank 0 -initial rank 0 -0 1704156354.2602494 -0 1704156354.2602494 -initial rank 0 -0 1704156354.2819088 -{} -{} -{} -{} +initial rank 2 diff --git a/spatial_decompose/job.sh b/spatial_decompose/job.sh index a1622bf..3158bb4 100644 --- a/spatial_decompose/job.sh +++ b/spatial_decompose/job.sh @@ -8,7 +8,5 @@ #SBATCH -t 00:05:00 conda activate deepmd-gpu -module load openmpi echo $(which mpiexec) -echo $(which mpirun) -mpirun -n 4 python MDargon_spatial.py \ No newline at end of file +mpiexec -n 4 python MDargon_spatial.py \ No newline at end of file From 893c0de285dfc5d4b87703faaad5e1c239cee94d Mon Sep 17 00:00:00 2001 From: Hancheng Zhao Date: Tue, 2 Jan 2024 18:42:07 -0500 Subject: [PATCH 2/9] spatial decomp working for 1st time step, add velocity into init file so that we can compare to others --- data/initial_position_LJ_argon256.txt | 512 +++++++++--------- init.txt | 0 spatial_decompose/LJ_SpatialDecomp.py | 3 +- spatial_decompose/MDargon_spatial.py | 64 ++- .../LJ_SpatialDecomp.cpython-39.pyc | Bin 1901 -> 1876 bytes .../__pycache__/utils_parallel.cpython-39.pyc | Bin 1270 -> 1146 bytes .../utils_spatial_decompose.cpython-39.pyc | Bin 9033 -> 8372 bytes spatial_decompose/job.out | 114 +++- .../results/argon256_Energy_Temp_Pres.csv | 3 + .../results/argon256_summary.txt | 6 + spatial_decompose/results/argon256iter1.txt | 256 +++++++++ spatial_decompose/utils_parallel.py | 69 +-- spatial_decompose/utils_spatial_decompose.py | 123 ++--- 13 files changed, 749 insertions(+), 401 deletions(-) create mode 100644 init.txt create mode 100644 spatial_decompose/results/argon256_Energy_Temp_Pres.csv create mode 100644 spatial_decompose/results/argon256_summary.txt create mode 100644 spatial_decompose/results/argon256iter1.txt diff --git a/data/initial_position_LJ_argon256.txt 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diff --git a/spatial_decompose/LJ_SpatialDecomp.py b/spatial_decompose/LJ_SpatialDecomp.py index 5eb4089..11f88ed 100644 --- a/spatial_decompose/LJ_SpatialDecomp.py +++ b/spatial_decompose/LJ_SpatialDecomp.py @@ -2,8 +2,7 @@ import numpy as np import utils_spatial_decompose as ut import utils_parallel as utp -def LJ_MD(subdiv,position_init,dt,stop_step,accel_init,r_cut,L,T_eq,e_scale,sig): - comm = MPI.COMM_WORLD +def LJ_MD(subdiv,position_init,dt,stop_step,accel_init,r_cut,L,T_eq,e_scale,sig, comm): rank = comm.Get_rank() #initialization if rank == 0: diff --git a/spatial_decompose/MDargon_spatial.py b/spatial_decompose/MDargon_spatial.py index 10f1937..a5aebff 100644 --- a/spatial_decompose/MDargon_spatial.py +++ b/spatial_decompose/MDargon_spatial.py @@ -10,8 +10,8 @@ k_B=1.38064852*10**(-23) dt=0.002 file_name='../data/initial_position_LJ_argon256.txt' -position_init=np.loadtxt(file_name) -num_atoms=position_init.shape[0] +info_init=np.loadtxt(file_name) +num_atoms=info_init.shape[0] a_init=np.zeros((num_atoms,3)) r_c=2.5 @@ -20,7 +20,7 @@ subdiv=np.array([2,2,1]) energy_scale=1.66*10**(-21)#unit: J, Argon sigma=3.4 #unit: Ang, Argon -T_dimensional_equal=123#unit K +T_dimensional_equal=300#unit K T_equal=T_dimensional_equal*k_B/energy_scale part_type='LJ' name='argon256' @@ -33,11 +33,10 @@ if rank==0: start_time = time.time() - # # initialize k_B=1.38064852*10**(-23) - size_sim=position_init.shape[0] - x_dot_init=ut.random_vel_generator(size_sim,T_equal,e_scale) + size_sim=info_init.shape[0] + # x_dot_init=ut.random_vel_generator(size_sim,T_equal,energy_scale) #initialize PE, KE, T_insta, P_insta, Momentum PE=np.zeros((stop_step+1,1)) KE=np.zeros((stop_step+1,1)) @@ -45,25 +44,54 @@ P_insta=np.zeros((stop_step+1,1)) #initialize the info matrix info=np.zeros((stop_step+1,size_sim,9)) - info[0,:,:]=np.concatenate((position_init,x_dot_init,accel_init),axis=1) - infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L) + # info[0,:,:]=np.concatenate((position_init,x_dot_init,a_init),axis=1) + info[0,:,:] = info_init + # np.savetxt('../data/init.txt',info[0,:,:],fmt='%.6f') + infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L0) #zero step value - PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_cut,L=L) + PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_c,L=L0) KE[0,:]=ut.Kin_Eng(info[0,:,3:6]) - T_insta[0,:]=2*KE[0,:]*e_scale/(3*(size_sim-1)*k_B) #k - P_insta[0,:]=ut.insta_pressure(L,T_insta[0],info[0,:,0:3],r_cut,e_scale) #unitless + T_insta[0,:]=2*KE[0,:]*energy_scale/(3*(size_sim-1)*k_B) #k + P_insta[0,:]=ut.insta_pressure(L0,T_insta[0],info[0,:,0:3],r_c,energy_scale) #unitless else: infotodic = None # info = None comm.barrier() infotodic = comm.bcast(infotodic, root = 0) +# Run MD +for step in range(stop_step): + my_spd_send=utp.vel_Ver( + comm = comm, + infodict=infotodic, + dt=dt, + r_limit=r_c, + L=L0, + my_rank=rank + ) + temp_infodict=comm.gather(my_spd_send,root=0) + if rank == 0: + temp_infodict=list(filter(None, temp_infodict)) + info_temp=dict(temp_infodict) + tmp=ut.concatDict(info_temp) + info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) + #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES + infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) + #calculate and store PE, KE, T_insta, P_insta + PE[step+1,:]=ut.LJ_potent_nondimen(info[step+1,:,0:3],r_cut=r_c,L=L0) + KE[step+1,:]=ut.Kin_Eng(info[step+1,:,3:6]) + T_insta[step+1,:]=2*KE[step+1,:]*energy_scale/(3*(size_sim-1)*k_B) #k + P_insta[step+1,:]=ut.insta_pressure(L0,T_insta[step+1],info[step+1,:,0:3],r_c,energy_scale) #unitless + comm.barrier() + infotodic=comm.bcast(infotodic,root=0) + if rank == 0: end_time = time.time() - print(f'Run time is {end_time-start_time:.3f}') + period = end_time-start_time + print(f'Run time is {period:.3f}') + ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, 1, False) comm.barrier() - # if rank==0: # start_time=time.time() # info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, @@ -81,13 +109,3 @@ # print("For this {} steps operation (dt={}) with r_cut = {} and L = {}, it took:".format(stop_step,dt,r_c,L0),end_time-start_time,'s') # ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, 1000, False) # else: -# LJ_MD(subdiv=subdiv, -# position_init=position_init, -# dt=dt, -# stop_step=stop_step, -# accel_init=a_init, -# r_cut=2.8, -# L=L0, -# T_eq=T_equal, -# e_scale=energy_scale, -# sig=sigma) diff --git a/spatial_decompose/__pycache__/LJ_SpatialDecomp.cpython-39.pyc b/spatial_decompose/__pycache__/LJ_SpatialDecomp.cpython-39.pyc index 53633ff7ee47b74c9a86a5a481522ae711812973..91c587eeccab82111108c544a0b37534b4b53ecf 100644 GIT binary patch delta 780 zcmZvZO=}b}9LAH$yzK6Dw%zV_x3#DgU!atFX`xn6f~}yUH^qX4ag()~?!1`E3Y82M z>b1}kKfq2sdGzGHM{k0sd;o8L2F;FokUEgbKTnb;zbE<8{MHP@AZP&d-J$R4*+~#W 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3.86672599e+00] + [ 7.75875596e-01 -1.02922664e-03 3.86928585e+00] + [ 7.72665905e-01 7.73425841e-01 3.09463953e+00] + [ 2.41338428e-04 5.02422428e-04 4.64373045e+00] + [-9.74451473e-04 7.74911452e-01 5.41352463e+00] + [ 7.71753970e-01 1.41585253e-03 5.41338492e+00] + [ 7.74637259e-01 7.77738079e-01 4.64195245e+00] + [ 1.27115284e-04 1.54822548e+00 -2.20172072e-03] + [ 4.34659549e-03 2.32106663e+00 7.68539864e-01] + [ 7.74949053e-01 1.54480560e+00 7.71903779e-01] + [ 7.73572924e-01 2.32191147e+00 2.16070349e-03] + [-1.32830472e-03 1.54800701e+00 1.54764453e+00] + [ 6.69767343e-04 2.32003255e+00 2.32247177e+00] + [ 7.71636667e-01 1.54884985e+00 2.31985073e+00] + [ 7.77311977e-01 2.31974593e+00 1.54604302e+00] + [ 1.20516131e-03 1.54821180e+00 3.09164525e+00] + [ 1.72408521e-03 2.31769829e+00 3.86746397e+00] + [ 7.75405965e-01 1.54797893e+00 3.87093365e+00] + [ 7.70744111e-01 2.32309487e+00 3.09335349e+00] + [ 2.65316546e-03 1.54936414e+00 4.64429247e+00] + [-7.27470586e-04 2.32051663e+00 5.41444788e+00] + [ 7.76604148e-01 1.54595709e+00 5.41606900e+00] + [ 7.74768095e-01 2.31910768e+00 4.64270518e+00] + [ 1.12610732e-03 3.09403446e+00 -2.45071268e-03] + [ 7.76905131e-01 3.09539269e+00 7.72038569e-01] + [ 2.82702131e-03 3.09632810e+00 1.54450374e+00] + [ 7.75289957e-01 3.09383230e+00 2.31812523e+00] + [-2.87714865e-03 3.09194406e+00 3.09311432e+00] + [ 7.75727295e-01 3.09632058e+00 3.86648888e+00] + [ 3.01662349e-03 3.09500762e+00 4.64068086e+00] + [ 7.76349828e-01 3.09607476e+00 5.41696620e+00] + [ 1.54715797e+00 9.89583284e-04 -1.27607272e-03] + [ 1.54809041e+00 7.70545371e-01 7.73598121e-01] + [ 2.32187654e+00 -1.16581451e-03 7.73918684e-01] + [ 2.31967170e+00 7.70874226e-01 -1.04841851e-03] + [ 1.54613949e+00 2.93865728e-03 1.54565282e+00] + [ 1.54788422e+00 7.74171951e-01 2.31796316e+00] + [ 2.32393607e+00 -7.13070657e-04 2.32320133e+00] + [ 2.31930778e+00 7.72104827e-01 1.54422085e+00] + [ 1.54282288e+00 -2.72980687e-04 3.09240500e+00] + [ 1.54394913e+00 7.72050671e-01 3.86720194e+00] + [ 2.32200123e+00 1.98579921e-03 3.86865341e+00] + [ 2.32385439e+00 7.67851153e-01 3.09536010e+00] + [ 1.54536990e+00 -7.70860543e-04 4.64162163e+00] + [ 1.54666834e+00 7.72392038e-01 5.41484616e+00] + [ 2.31885612e+00 -5.91685861e-05 5.41247594e+00] + [ 2.32380066e+00 7.74121689e-01 4.64166313e+00] + [ 1.54745628e+00 1.54807116e+00 -5.85834719e-04] + [ 1.54740722e+00 2.31983776e+00 7.74095041e-01] + [ 2.32136871e+00 1.54731097e+00 7.75491615e-01] + [ 2.32315449e+00 2.31891209e+00 4.58589343e-04] + [ 1.54493402e+00 1.54780211e+00 1.54603322e+00] + [ 1.54985712e+00 2.31971950e+00 2.31685217e+00] + [ 2.31928431e+00 1.54858220e+00 2.31991379e+00] + [ 2.32312406e+00 2.31782385e+00 1.54407053e+00] + [ 1.54758474e+00 1.54717233e+00 3.09601167e+00] + [ 1.54299452e+00 2.32145341e+00 3.86692722e+00] + [ 2.32216576e+00 1.54524505e+00 3.86944472e+00] + [ 2.31932396e+00 2.31901210e+00 3.08996472e+00] + [ 1.54640209e+00 1.54897516e+00 4.64248851e+00] + [ 1.54477983e+00 2.32139829e+00 5.41722926e+00] + [ 2.31956168e+00 1.54466800e+00 5.41816568e+00] + [ 2.31840834e+00 2.31969079e+00 4.64344552e+00] + [ 1.54812465e+00 3.09661388e+00 -8.74368687e-04] + [ 2.32173424e+00 3.09286371e+00 7.73936193e-01] + [ 1.54892724e+00 3.09680736e+00 1.54782162e+00] + [ 2.32359470e+00 3.09534898e+00 2.32178393e+00] + [ 1.54888117e+00 3.09498662e+00 3.09251277e+00] + [ 2.31875835e+00 3.09257155e+00 3.86967640e+00] + [ 1.54396071e+00 3.09542554e+00 4.63851839e+00] + [ 2.32038274e+00 3.09226142e+00 5.41562997e+00] + [ 3.09262635e+00 -3.26260685e-04 4.43386132e-03] + [ 3.09067396e+00 7.71196651e-01 7.73481519e-01] + [ 3.09490834e+00 4.77703313e-04 1.54525342e+00] + [ 3.09261101e+00 7.75353045e-01 2.32431201e+00] + [ 3.09331749e+00 8.56155345e-04 3.09191875e+00] + [ 3.09841611e+00 7.75847465e-01 3.86487803e+00] + [ 3.09521262e+00 4.23613490e-04 4.64009969e+00] + [ 3.09357502e+00 7.75228256e-01 5.41670122e+00] + [ 3.09501006e+00 1.54725506e+00 3.52530731e-03] + [ 3.09640266e+00 2.31970704e+00 7.73528575e-01] + [ 3.09670456e+00 1.54802370e+00 1.54652535e+00] + [ 3.08859863e+00 2.32450766e+00 2.31996533e+00] + [ 3.09378521e+00 1.54545742e+00 3.09538688e+00] + [ 3.09384318e+00 2.32205758e+00 3.86659412e+00] + [ 3.09379228e+00 1.54909891e+00 4.64262336e+00] + [ 3.09367429e+00 2.31842039e+00 5.41668680e+00] + [ 3.09225760e+00 3.09940750e+00 1.27173935e-03] + [ 3.09500896e+00 3.09479678e+00 1.54778235e+00] + [ 3.09195218e+00 3.09196117e+00 3.09123261e+00] + [ 3.09427921e+00 3.09304485e+00 4.64076743e+00]] +Run time is 1.369 +results/argon256iter1.txt +1 4 +1 4 +2 4 +2 4 +3 4 +3 4 diff --git a/spatial_decompose/results/argon256_Energy_Temp_Pres.csv b/spatial_decompose/results/argon256_Energy_Temp_Pres.csv new file mode 100644 index 0000000..78f2fd7 --- /dev/null +++ b/spatial_decompose/results/argon256_Energy_Temp_Pres.csv @@ -0,0 +1,3 @@ +step,KE,PE,T_insta,P_insta +0,391.301575210033,-1337.5726394999983,123.00000045477438,1.4292896176688794 +1,390.80152710093626,-1337.0729278505548,122.84281755150266,1.4403740455155791 diff --git a/spatial_decompose/results/argon256_summary.txt b/spatial_decompose/results/argon256_summary.txt new file mode 100644 index 0000000..c08f4ad --- /dev/null +++ b/spatial_decompose/results/argon256_summary.txt @@ -0,0 +1,6 @@ +Simulation Cell Size(unitless): 6.8 +Simulation Particles Amount: 256 +File Name: argon256 +Simulation Time: 1.3687632083892822 +Simulation Step: 1 +Force Cut-off: 2.5 diff --git a/spatial_decompose/results/argon256iter1.txt b/spatial_decompose/results/argon256iter1.txt new file mode 100644 index 0000000..fb330ad --- /dev/null +++ b/spatial_decompose/results/argon256iter1.txt @@ -0,0 +1,256 @@ +6.799592 6.796485 0.001309 -0.206446 -1.759622 0.651945 -2.222341 -2.235431 -2.339640 +6.799155 0.772494 0.774807 -0.429318 -0.515865 0.639765 -6.694153 1.580255 0.856371 +0.775929 6.799016 0.773862 1.200720 -0.498982 0.168211 0.529862 -6.972901 1.559090 +0.776434 0.772369 0.002444 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+5.418102 4.644765 3.868645 1.704514 1.792184 0.498327 6.391065 -2.484729 -0.702418 +5.413122 5.413930 3.093923 -0.787188 -0.383419 -0.097480 4.630620 4.605196 -0.205497 +4.643750 4.639460 4.640964 1.284162 -0.859307 -0.107243 -2.959562 -1.467297 -1.376067 +4.640251 5.412183 5.411784 -0.463653 -1.256309 -1.456133 -1.266626 5.226391 4.954895 +5.415626 4.641704 5.413973 0.465188 0.262567 -0.361731 5.105880 -1.247840 4.921133 +5.413970 5.414551 4.640618 -0.362967 -0.072056 -0.279934 5.127361 5.237874 -0.970856 diff --git a/spatial_decompose/utils_parallel.py b/spatial_decompose/utils_parallel.py index b4cbefa..bc5fa2c 100644 --- a/spatial_decompose/utils_parallel.py +++ b/spatial_decompose/utils_parallel.py @@ -5,44 +5,35 @@ import functools import operator #@numba.njit() ##This might not be needed -def par_worker_vel_ver_pre(infodict,dt,r_limit,L): - vel_Ver(infodict,dt,r_limit,L) +def par_worker_vel_ver_pre(comm,infodict,dt,r_limit,L,my_rank): + vel_Ver(comm,infodict,dt,r_limit,L,my_rank) #@numba.njit() -def vel_Ver(infodict,dt,r_limit=2.5,L=6.8): - comm = MPI.COMM_WORLD - rank = comm.Get_rank() - size = comm.Get_size() - if rank!=0: - ## Get the data for the current spatial domain - my_spd, neighs_spd=ut.separate_points(infodict, rank) - #acceleration at 0 - my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L) - #velocity at dt/2 - my_spd.V=my_spd.V+my_spd.A*(dt/2) - #position at dt - my_spd.P=my_spd.P+my_spd.V*dt - #PBC rule 1 - my_spd.P=ut.pbc1(position=my_spd.P,L=L) - my_spd_send=(rank,my_spd) - else: - my_spd_send=None - comm.barrier() - temp_infodict=comm.allgather(my_spd_send) - if rank!=0: - temp_infodict=list(filter(None, temp_infodict)) - infodict=dict(temp_infodict) - my_spd, neighs_spd=ut.separate_points(infodict, rank) - #acceleration at dt - my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L) - #velocity at dt - my_spd.V=my_spd.V+my_spd.A*(dt/2) - my_spd_send=(rank,my_spd) - else: - my_spd_send=None - comm.barrier() - temp_infodict=comm.gather(my_spd_send,root=0) - if rank==0: - temp_infodict=list(filter(None, temp_infodict)) - infodict=dict(temp_infodict) - return infodict +def vel_Ver(comm,infodict,dt,r_limit=2.5,L=6.8,my_rank=0): + # rank = comm.Get_rank() + rank = my_rank + size = comm.Get_size() + print(rank,size) + ## Get the data for the current spatial domain + my_spd, neighs_spd=ut.separate_points(infodict, rank, size) + # LEAP FROG METHOD + #acceleration at 0 + my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L) + #velocity at dt/2 + my_spd.V=my_spd.V+my_spd.A*(dt/2) + #position at dt + my_spd.P=my_spd.P+my_spd.V*dt + if rank==0: + print('before pbc1 ',my_spd.P) + #PBC rule 1 + my_spd.P=ut.pbc1(position=my_spd.P,L=L) + my_spd_send=(rank,my_spd) + comm.barrier() + temp_infodict=comm.allgather(my_spd_send) + # acceleration at dt + my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L) + # velocity at dt + my_spd.V=my_spd.V+my_spd.A*(dt/2) + my_spd_send=(rank,my_spd) + comm.barrier() + return my_spd_send diff --git a/spatial_decompose/utils_spatial_decompose.py b/spatial_decompose/utils_spatial_decompose.py index 65f07d3..b7aa949 100644 --- a/spatial_decompose/utils_spatial_decompose.py +++ b/spatial_decompose/utils_spatial_decompose.py @@ -185,23 +185,23 @@ def cell_to_dict(info,nx,ny,nz,L): yinterval=L/ny zinterval=L/nz #cell_lists={} - for i in range(1,nx*ny*nz+1): + for i in range(nx*ny*nz): cell_dict[i]= np.zeros((1,9)) for i in range(info.shape[0]): atom=info[i,0:9].reshape(1,9) #check extra one!!! #if statements !!!!!!! #check later - atomID=int(((np.floor(atom[:,0]/xinterval)+1+(np.floor(atom[:,1]/yinterval))*ny)+(np.floor(atom[:,2]/zinterval))*(nx*ny))[0]) + atomID=int(((np.floor(atom[:,0]/xinterval)+(np.floor(atom[:,1]/yinterval))*ny)+(np.floor(atom[:,2]/zinterval))*(nx*ny))[0]) cell_dict[atomID]=np.append(cell_dict[atomID],atom,axis=0) - for i in range(1,nx*ny*nz+1): + for i in range(nx*ny*nz): cell_dict[i]=cell_dict[i][1:,:] return cell_dict def cell_to_obj(positions,nx,ny,nz,L): cell_lists=cell_to_dict(positions,nx,ny,nz,L) new_cell_list={} - for i in range(1,nx*ny*nz+1): + for i in range(nx*ny*nz): # I think this works but we should think more about what an "empty" shape means # currently when a key points to an empty cube the cube has a position vector of dimensions [0,3] if cell_lists[i].shape[0]!=0: @@ -222,7 +222,7 @@ def cell_to_obj(positions,nx,ny,nz,L): #@numba.njit() def separate_points(infodict, my_rank, nproc): - neighbor_spd = None + neighb_spd = None # Processor matrix n*n*1 (for comparison with force decomposition) axis = np.sqrt(nproc) # Here we need to be careful about only copying the neighboring subcube @@ -246,6 +246,7 @@ def separate_points(infodict, my_rank, nproc): elif i == axis: i = i - axis neighbor_rank[t] = (xy[0] + xy[1]*axis) + # print('neighboring ',my_rank, neighbor_rank) # copy the info in neighboring ranks for i, spd in infodict.items(): @@ -297,80 +298,48 @@ def data_saver(info, PE, KE, T_insta, P_insta, L, num_atoms,part_type,name,perio iterations=str(iterations_int) if make_directory == True: os.mkdir('results') - # path_to_file_xyz="results/"+name+"position_last"+iterations+"stps"+".xyz" - path_to_file_xyz = "results/"+name+"iter"+iterations+'.txt' - path_to_file_other = "results/"+name+"_Energy_Temp_Pres"+".csv" - path_to_file_summary = "results/"+name+"_summary"+".txt" - p= open(path_to_file_xyz,"w") - s= open(path_to_file_summary,'w') + # path_to_file_xyz="results/"+name+"position_last"+iterations+"stps"+".xyz" + path_to_file_xyz = "results/"+name+"iter"+iterations+'.txt' + path_to_file_other = "results/"+name+"_Energy_Temp_Pres"+".csv" + path_to_file_summary = "results/"+name+"_summary"+".txt" + p= open(path_to_file_xyz,"w") + s= open(path_to_file_summary,'w') - # #writing xyz file - # comment = 'This is the position of the system during the last '+iterations+' steps' - # # for atoms in info[-int(iterations):,:,:]: - # p.write("%s\n" % str(num_atoms)) - # p.write("%s\n" % comment) - # for atom in atoms: - # # p.write(part_type) - # p.write("\t%s\n" % str(atom)[1:-2]) + # #writing xyz file + # comment = 'This is the position of the system during the last '+iterations+' steps' + # # for atoms in info[-int(iterations):,:,:]: + # p.write("%s\n" % str(num_atoms)) + # p.write("%s\n" % comment) + # for atom in atoms: + # # p.write(part_type) + # p.write("\t%s\n" % str(atom)[1:-2]) - #writing xyz file - comment = 'This is the position of the system of the final step' - # for atoms in info[-int(iterations):,:,:]: - # p.write("%s\n" % str(num_atoms)) - # p.write("%s\n" % comment) - # for i in range(num_atoms): - # p.write("\t%s\n" % str(info[:])) - np.savetxt(path_to_file_xyz,info[-1,:,:]) + #writing xyz file + comment = 'This is the position of the system of the final step' + print(path_to_file_xyz) + # for atoms in info[-int(iterations):,:,:]: + # p.write("%s\n" % str(num_atoms)) + # p.write("%s\n" % comment) + # for i in range(num_atoms): + # p.write("\t%s\n" % str(info[:])) + np.savetxt(path_to_file_xyz,info[-1,:,:],fmt='%.6f') - #writing other file - other_dict={} - other_dict['KE']=KE.reshape(KE.shape[0],) - other_dict['PE']=PE.reshape(PE.shape[0],) - other_dict['T_insta']=T_insta.reshape(T_insta.shape[0],) - other_dict['P_insta']=P_insta.reshape(P_insta.shape[0],) - other_df=pd.DataFrame.from_dict(other_dict) - other_df.to_csv(path_to_file_other,index_label='step') + #writing other file + other_dict={} + other_dict['KE']=KE.reshape(KE.shape[0],) + other_dict['PE']=PE.reshape(PE.shape[0],) + other_dict['T_insta']=T_insta.reshape(T_insta.shape[0],) + other_dict['P_insta']=P_insta.reshape(P_insta.shape[0],) + other_df=pd.DataFrame.from_dict(other_dict) + other_df.to_csv(path_to_file_other,index_label='step') - #writing summary file - s.write("Simulation Cell Size(unitless): "+str(L)+"\n") - s.write("Simulation Particles Amount: "+str(num_atoms)+"\n") - s.write("File Name: "+str(name)+"\n") - s.write("Simulation Time: "+ str(period)+"\n") - s.write("Simulation Step: "+str(stop_step)+"\n") - s.write("Force Cut-off: "+str(r_c)+"\n") - p.close() - s.close() - else: - path_to_file_xyz="results/"+name+"position_last"+iterations+"stps"+".xyz" - path_to_file_other = "results/"+name+"_Energy_Temp_Pres"+".csv" - path_to_file_summary = "results/"+name+"_summary"+".txt" - p= open(path_to_file_xyz,"w") - s= open(path_to_file_summary,'w') - - #writing xyz file - comment = 'This is the position of the system during the last '+iterations+' steps' - for atoms in info[-int(iterations):,:,0:3]: - p.write("%s\n" % str(num_atoms)) - p.write("%s\n" % comment) - for atom in atoms: - p.write(part_type) - p.write("\t%s\n" % str(atom)[1:-2]) - - #writing other file - other_dict={} - other_dict['KE']=KE.reshape(KE.shape[0],) - other_dict['PE']=PE.reshape(PE.shape[0],) - other_dict['T_insta']=T_insta.reshape(T_insta.shape[0],) - other_dict['P_insta']=P_insta.reshape(P_insta.shape[0],) - other_df=pd.DataFrame.from_dict(other_dict) - other_df.to_csv(path_to_file_other,index_label='step') + #writing summary file + s.write("Simulation Cell Size(unitless): "+str(L)+"\n") + s.write("Simulation Particles Amount: "+str(num_atoms)+"\n") + s.write("File Name: "+str(name)+"\n") + s.write("Simulation Time: "+ str(period)+"\n") + s.write("Simulation Step: "+str(stop_step)+"\n") + s.write("Force Cut-off: "+str(r_c)+"\n") + p.close() + s.close() - #writing summary file - s.write("Simulation Cell Size(unitless): "+str(L)+"\n") - s.write("Simulation Particles Amount: "+str(num_atoms)+"\n") - s.write("File Name: "+str(name)+"\n") - s.write("Simulation Time: "+ str(period)+"\n") - s.write("Simulation Step: "+str(stop_step)+"\n") - s.write("Force Cut-off: "+str(r_c)+"\n") - p.close() - s.close() From 78dd81ba6dd79518d79e6a35a27b05a57e9e5a96 Mon Sep 17 00:00:00 2001 From: Hancheng Zhao Date: Tue, 2 Jan 2024 19:51:26 -0500 Subject: [PATCH 3/9] 1000 timesteps converged, used as reference for other decomp --- spatial_decompose/MDargon_spatial.py | 8 +- .../__pycache__/utils_parallel.cpython-39.pyc | Bin 1146 -> 1084 bytes .../utils_spatial_decompose.cpython-39.pyc | Bin 8372 -> 8372 bytes spatial_decompose/job.out | 208 ++-- spatial_decompose/job.sh | 2 +- .../results/argon256_Energy_Temp_Pres.csv | 999 ++++++++++++++++++ .../results/argon256_summary.txt | 4 +- spatial_decompose/results/argon256iter1.txt | 512 ++++----- .../results/argon256iter1000.txt | 256 +++++ spatial_decompose/utils_parallel.py | 3 - spatial_decompose/utils_spatial_decompose.py | 2 +- 11 files changed, 1622 insertions(+), 372 deletions(-) create mode 100644 spatial_decompose/results/argon256iter1000.txt diff --git a/spatial_decompose/MDargon_spatial.py b/spatial_decompose/MDargon_spatial.py index a5aebff..6dff803 100644 --- a/spatial_decompose/MDargon_spatial.py +++ b/spatial_decompose/MDargon_spatial.py @@ -6,7 +6,7 @@ from mpi4py import MPI # run params -stop_step=1 +stop_step=1000 k_B=1.38064852*10**(-23) dt=0.002 file_name='../data/initial_position_LJ_argon256.txt' @@ -71,6 +71,8 @@ ) temp_infodict=comm.gather(my_spd_send,root=0) if rank == 0: + if step%10==0: + print('current time step is ', step) temp_infodict=list(filter(None, temp_infodict)) info_temp=dict(temp_infodict) tmp=ut.concatDict(info_temp) @@ -88,8 +90,8 @@ if rank == 0: end_time = time.time() period = end_time-start_time - print(f'Run time is {period:.3f}') - ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, 1, False) + print(f'Run time is {period:.3f} seconds') + ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, stop_step, False) comm.barrier() # if rank==0: diff --git a/spatial_decompose/__pycache__/utils_parallel.cpython-39.pyc b/spatial_decompose/__pycache__/utils_parallel.cpython-39.pyc index e5544e3760a8318931c71945bb751cc8b6d28b73..56d1d0a0cc2d55ff2c198b666aeaee75962c7311 100644 GIT binary patch delta 295 zcmb7?O-QnDxIu%EdbS!uP#Z8iiP41r3Cx!WAiMtV!dZDM&~w zoH>;lYijP43tY0wI5HNSM@j`fKnL!?=!sa@I&>v$`^lMd;g)1GZ0hn#!Q0J|G=N}9 zs=mQ+^Uq^{LKhuBf}HD5dg|pgzqQxqVj=ej8I;xdZMrDyU)r=D4FWL=wOx<8)UJ1K Jh@JYLCr3Z%LSg^_ delta 371 zcmb7=u};H442FHapd}}= zt`2uuahp Date: Wed, 3 Jan 2024 19:28:24 -0500 Subject: [PATCH 4/9] spatial decomp only one bug left: pbc not working as expected. Also a bug in mpirun on bridges makes debugging impossible --- atom_decompose/AtomicDecomp.py | 49 ---- atom_decompose/LJ_AtomicDecomp.py | 51 ++++ atom_decompose/MDargon_atomic.py | 113 ++++++++ atom_decompose/utils_atomic_decompose.py | 215 +++++++++++++++ atom_decompose/utils_parallel.py | 36 +++ spatial_decompose/MDargon_spatial.py | 27 +- .../LJ_SpatialDecomp.cpython-39.pyc | Bin 1876 -> 1876 bytes ...patialDecomp.cpython-39.pyc.23407409052528 | 0 .../__pycache__/utils_parallel.cpython-39.pyc | Bin 1084 -> 974 bytes .../utils_spatial_decompose.cpython-39.pyc | Bin 8372 -> 8567 bytes spatial_decompose/job.err | 3 + spatial_decompose/job.out | 108 +------- spatial_decompose/job.sh | 8 +- .../argon256_Energy_Temp_Pres16core.csv | 12 + .../argon256_Energy_Temp_Pres4core.csv | 12 + .../results/argon256core16_summary.txt | 6 + .../results/argon256core4_summary.txt | 6 + .../results/argon256iter10core16.txt | 256 ++++++++++++++++++ .../results/argon256iter10core4.txt | 256 ++++++++++++++++++ .../results/argon256iter1core4.txt | 256 ++++++++++++++++++ .../results/argon256iter2core16.txt | 256 ++++++++++++++++++ .../results/argon256iter2core4.txt | 256 ++++++++++++++++++ spatial_decompose/temp.txt | 20 ++ spatial_decompose/utils_parallel.py | 19 +- spatial_decompose/utils_spatial_decompose.py | 67 +++-- 25 files changed, 1836 insertions(+), 196 deletions(-) delete mode 100644 atom_decompose/AtomicDecomp.py create mode 100644 atom_decompose/LJ_AtomicDecomp.py create mode 100644 atom_decompose/MDargon_atomic.py create mode 100644 atom_decompose/utils_atomic_decompose.py create mode 100644 atom_decompose/utils_parallel.py create mode 100644 spatial_decompose/__pycache__/LJ_SpatialDecomp.cpython-39.pyc.23407409052528 create mode 100644 spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv create mode 100644 spatial_decompose/results/argon256_Energy_Temp_Pres4core.csv create mode 100644 spatial_decompose/results/argon256core16_summary.txt create mode 100644 spatial_decompose/results/argon256core4_summary.txt create mode 100644 spatial_decompose/results/argon256iter10core16.txt create mode 100644 spatial_decompose/results/argon256iter10core4.txt create mode 100644 spatial_decompose/results/argon256iter1core4.txt create mode 100644 spatial_decompose/results/argon256iter2core16.txt create mode 100644 spatial_decompose/results/argon256iter2core4.txt create mode 100644 spatial_decompose/temp.txt diff --git a/atom_decompose/AtomicDecomp.py b/atom_decompose/AtomicDecomp.py deleted file mode 100644 index 6eeee98..0000000 --- a/atom_decompose/AtomicDecomp.py +++ /dev/null @@ -1,49 +0,0 @@ -import numpy as np -import numba -from numba.experimental import jitclass -from numba import float64 -from numba.typed import Dict -from numba.core import types -import os -import pandas as pd -import copy -from utils import SpatialDomainData as spd - -def cell_to_dict_atom(info,ncore): - cell_lists = Dict.empty(key_type=types.int64, value_type=float_array) - for i in range(1,ncore+1): - cell_lists[i] = np.zeros((1,9)) - for i in range(info.shape[0]): - # atomic coordinates, velocity and acceleration - atom = info[i,0:9].reshape(1,9) - atomID = int(np.floor(i*ncore/info.shape[0])) + 1 - cell_lists[atomID] = np.append(cell_lists[atomID],atom,axis=0) - # for i in range(1,ncore): - # cell_lists[i] = cell_lists[i][1:,:] - return cell_lists - -def cell_to_obj_atom(info,ncore): - cell_lists = cell_to_dict_atom(info,ncore) - new_cell_list = {} - for i in range(1, ncore+1): - if cell_lists[i].shape[0]!=0: - pos = cell_lists[i][:,0:3] # position - vel = cell_lists[i][:,3:6] # velocity - acc = cell_lists[i][:,6:9] # acceleration - spatial_domain_data = spd(pos, vel, acc) - new_cell_list[i] = spatial_domain_data - else: - new_cell_list[i] = spd(np.empty((0,3)),np.empty((0,3)),np.empty((0,3))) - return new_cell_list - -def separate_points_atom(infodict,my_rank): - # since we are using atom-wise decomposition, each processor must know every atomic position - neighbor_spd = None - for i, spd in infodict.items(): - if i!=my_rank: - if neighbor_spd is None: - neighbor_spd = copy.deepcopy(spd) - else: - neighbor_spd.concat(spd) - return infodict[my_rank], neighbor_spd - diff --git a/atom_decompose/LJ_AtomicDecomp.py b/atom_decompose/LJ_AtomicDecomp.py new file mode 100644 index 0000000..11f88ed --- /dev/null +++ b/atom_decompose/LJ_AtomicDecomp.py @@ -0,0 +1,51 @@ +from mpi4py import MPI +import numpy as np +import utils_spatial_decompose as ut +import utils_parallel as utp +def LJ_MD(subdiv,position_init,dt,stop_step,accel_init,r_cut,L,T_eq,e_scale,sig, comm): + rank = comm.Get_rank() + #initialization + if rank == 0: + k_B=1.38064852*10**(-23) + size_sim=position_init.shape[0] + x_dot_init=ut.random_vel_generator(size_sim,T_eq,e_scale) + #initialize PE, KE, T_insta, P_insta, Momentum + PE=np.zeros((stop_step+1,1)) + KE=np.zeros((stop_step+1,1)) + T_insta=np.zeros((stop_step+1,1)) + P_insta=np.zeros((stop_step+1,1)) + #initialize the info matrix + info=np.zeros((stop_step+1,size_sim,9)) + info[0,:,:]=np.concatenate((position_init,x_dot_init,accel_init),axis=1) + infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L) + #zero step value + PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_cut,L=L) + KE[0,:]=ut.Kin_Eng(info[0,:,3:6]) + T_insta[0,:]=2*KE[0,:]*e_scale/(3*(size_sim-1)*k_B) #k + P_insta[0,:]=ut.insta_pressure(L,T_insta[0],info[0,:,0:3],r_cut,e_scale) #unitless + + + else: + infotodic=None + comm.barrier() + infotodic=comm.bcast(infotodic,root=0) + for step in range(stop_step): + if rank!=0: + #call the vel_verlet parallel function + utp.par_worker_vel_ver_pre(infotodic,dt,r_cut,L) + else: + info_temp=utp.vel_Ver(infodict=infotodic,dt=dt,r_limit=r_cut,L=L) + print(info_temp) + tmp=ut.concatDict(info_temp) + info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) + #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES + infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L) + #calculate and store PE, KE, T_insta, P_insta + PE[step+1,:]=ut.LJ_potent_nondimen(info[step+1,:,0:3],r_cut=r_cut,L=L) + KE[step+1,:]=ut.Kin_Eng(info[step+1,:,3:6]) + T_insta[step+1,:]=2*KE[step+1,:]*e_scale/(3*(size_sim-1)*k_B) #k + P_insta[step+1,:]=ut.insta_pressure(L,T_insta[step+1],info[step+1,:,0:3],r_cut,e_scale) #unitless + comm.barrier() + infotodic=comm.bcast(infotodic,root=0) + if rank==0: + return info,PE,KE,T_insta,P_insta diff --git a/atom_decompose/MDargon_atomic.py b/atom_decompose/MDargon_atomic.py new file mode 100644 index 0000000..6dff803 --- /dev/null +++ b/atom_decompose/MDargon_atomic.py @@ -0,0 +1,113 @@ +import numpy as np +import time +import copy +from LJ_SpatialDecomp import * +import utils_spatial_decompose as ut +from mpi4py import MPI + +# run params +stop_step=1000 +k_B=1.38064852*10**(-23) +dt=0.002 +file_name='../data/initial_position_LJ_argon256.txt' +info_init=np.loadtxt(file_name) +num_atoms=info_init.shape[0] + +a_init=np.zeros((num_atoms,3)) +r_c=2.5 +L0=6.8 +#cube division +subdiv=np.array([2,2,1]) +energy_scale=1.66*10**(-21)#unit: J, Argon +sigma=3.4 #unit: Ang, Argon +T_dimensional_equal=300#unit K +T_equal=T_dimensional_equal*k_B/energy_scale +part_type='LJ' +name='argon256' + +comm = MPI.COMM_WORLD +rank = comm.Get_rank() +size = comm.Get_size() +print(rank,size) +comm.barrier() + +if rank==0: + start_time = time.time() + # # initialize + k_B=1.38064852*10**(-23) + size_sim=info_init.shape[0] + # x_dot_init=ut.random_vel_generator(size_sim,T_equal,energy_scale) + #initialize PE, KE, T_insta, P_insta, Momentum + PE=np.zeros((stop_step+1,1)) + KE=np.zeros((stop_step+1,1)) + T_insta=np.zeros((stop_step+1,1)) + P_insta=np.zeros((stop_step+1,1)) + #initialize the info matrix + info=np.zeros((stop_step+1,size_sim,9)) + # info[0,:,:]=np.concatenate((position_init,x_dot_init,a_init),axis=1) + info[0,:,:] = info_init + # np.savetxt('../data/init.txt',info[0,:,:],fmt='%.6f') + infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L0) + #zero step value + PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_c,L=L0) + KE[0,:]=ut.Kin_Eng(info[0,:,3:6]) + T_insta[0,:]=2*KE[0,:]*energy_scale/(3*(size_sim-1)*k_B) #k + P_insta[0,:]=ut.insta_pressure(L0,T_insta[0],info[0,:,0:3],r_c,energy_scale) #unitless +else: + infotodic = None + # info = None +comm.barrier() +infotodic = comm.bcast(infotodic, root = 0) + +# Run MD +for step in range(stop_step): + my_spd_send=utp.vel_Ver( + comm = comm, + infodict=infotodic, + dt=dt, + r_limit=r_c, + L=L0, + my_rank=rank + ) + temp_infodict=comm.gather(my_spd_send,root=0) + if rank == 0: + if step%10==0: + print('current time step is ', step) + temp_infodict=list(filter(None, temp_infodict)) + info_temp=dict(temp_infodict) + tmp=ut.concatDict(info_temp) + info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) + #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES + infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) + #calculate and store PE, KE, T_insta, P_insta + PE[step+1,:]=ut.LJ_potent_nondimen(info[step+1,:,0:3],r_cut=r_c,L=L0) + KE[step+1,:]=ut.Kin_Eng(info[step+1,:,3:6]) + T_insta[step+1,:]=2*KE[step+1,:]*energy_scale/(3*(size_sim-1)*k_B) #k + P_insta[step+1,:]=ut.insta_pressure(L0,T_insta[step+1],info[step+1,:,0:3],r_c,energy_scale) #unitless + comm.barrier() + infotodic=comm.bcast(infotodic,root=0) + +if rank == 0: + end_time = time.time() + period = end_time-start_time + print(f'Run time is {period:.3f} seconds') + ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, stop_step, False) +comm.barrier() + +# if rank==0: +# start_time=time.time() +# info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, +# position_init=position_init, +# dt=dt, +# stop_step=stop_step, +# accel_init=a_init, +# r_cut=2.8, +# L=L0, +# T_eq=T_equal, +# e_scale=energy_scale, +# sig=sigma) +# end_time=time.time() +# period = end_time-start_time +# print("For this {} steps operation (dt={}) with r_cut = {} and L = {}, it took:".format(stop_step,dt,r_c,L0),end_time-start_time,'s') +# ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, 1000, False) +# else: diff --git a/atom_decompose/utils_atomic_decompose.py b/atom_decompose/utils_atomic_decompose.py new file mode 100644 index 0000000..c59dd5d --- /dev/null +++ b/atom_decompose/utils_atomic_decompose.py @@ -0,0 +1,215 @@ +import numpy as np +import numba +from numba.experimental import jitclass +from numba import float64 +from numba.typed import Dict +from numba.core import types +import os +import pandas as pd +import copy +from utils import SpatialDomainData as spd + +class SpatialDomainData: + #This class creates objects for storing position, velocity and acceleration information + ##This class contain three functions: + ###__init__ (description) + ###__repr__ (description) + ###concat(description) + def __init__(self, position=np.array([]), velocity=np.array([]), acceleration=np.array([])): + self.P = position + self.V = velocity + self.A = acceleration + + def __repr__(self): + return "(P:{}, V:{}, A:{})".format(self.P, self.V, self.A) + + def concat(self, other): + self.P = np.concatenate((self.P, other.P), 0) + self.V = np.concatenate((self.V, other.V), 0) + self.A = np.concatenate((self.A, other.A), 0) + +# @numba.njit +def pbc1(position,L): + ##This function perform the first rule of periodic boundary condition + #Input: position -- the position before PBC1 + # L -- the simulation cell size + #Ouput: x_new -- the updated position after PBC1 + position_new=np.zeros((position.shape[0],3)) + for i in range(position.shape[0]): + position_ind=position[i,:] + position_empty=np.zeros((1,3)) + for j in range(3): + # position_axis=numba.float64(position_ind[j]) + position_axis = position_ind[j] + if position_axis < 0: + position_axis_new=position_axis+L + elif position_axis > L: + position_axis_new=position_axis-L + else: + position_axis_new=position_axis + position_empty[:,j]=position_axis_new + position_new[i,:]=position_empty + return position_new + +# @numba.njit +def pbc2(separation,L): + ##This function perform the second rule of periodic boundary condition + #Input: separation -- separation before PBC2 + # L -- the simulation cell size + #Ouput: separation_new -- the updated separation after PBC2 + separation_new=np.zeros((separation.shape[0],3)) + for i in range(separation.shape[0]): + separation_ind=separation[i,:] + separation_empty=np.zeros((1,3)) + for j in range(3): + # separation_axis=numba.float64(separation_ind[j]) + separation_axis = separation_ind[j] + if separation_axis < -L/2: + separation_axis_new=separation_axis+L + elif separation_axis > L/2: + separation_axis_new=separation_axis-L + else: + separation_axis_new=separation_axis + separation_empty[:,j]=separation_axis_new + separation_new[i,:]=separation_empty + return separation_new + +# @numba.njit +def random_vel_generator(n,T_equal,e_scale): + ##This function generate random initial velocity at the desired temperature + #Input: n -- number of atoms + # T_equal -- the temperature of interests + # e_scale -- the energy scale of the particle of interests + #Ouput: vel_per_particle -- the velocity matrix assigned to all particles + total_k=3*T_equal*(n-1)/2 + vel_per_particle=np.zeros((n,3)) + for axis in range(3): + vel_per_particle[:,axis]=np.random.randn(n,)-0.5 + Mom_x_total=np.sum(vel_per_particle[:,0]) + Mom_y_total=np.sum(vel_per_particle[:,1]) + Mom_z_total=np.sum(vel_per_particle[:,2]) + Mom_x_avg=Mom_x_total/n + Mom_y_avg=Mom_y_total/n + Mom_z_avg=Mom_z_total/n + vel_per_particle=vel_per_particle-np.array([Mom_x_avg,Mom_y_avg,Mom_z_avg]).reshape(1,3) + k_avg_init=0.5*(1/n)*np.sum(np.sum(vel_per_particle**2,axis=1),axis=0) + k_avg_T_eq=total_k/n + scaling_ratio=np.sqrt(k_avg_T_eq/k_avg_init) + vel_per_particle=vel_per_particle*scaling_ratio + return vel_per_particle + +# @numba.njit +def Kin_Eng(velocity): + ##This function compute the average kinetic energy of the system at given the velocity + #Input: velocity -- the velocities of all the particles + #Output: Kinetic_sum -- the average kinetic energy of the system + num=velocity.shape[0] + Kinetic_per=0.5*np.sum(velocity**2,axis=1) + Kinetic_avg=np.sum(Kinetic_per,axis=0) + return Kinetic_avg + +# @numba.njit +def LJ_potent_nondimen(position,r_cut,L): + ##This function compute the nondimensional potential energy of the system at the given position + #Input: position -- the position of all the particles at this instance + # r_cut -- the cutoff for the short-range force field + # L -- the size of the simulation cell + #Output: np.sum(update_LJ) -- the potential energy of the system at this instance + num=position.shape[0] + update_LJ=np.zeros((num-1,1)) + #fix value for a certain r_limit + dU_drcut=24*r_cut**(-7)-48*r_cut**(-13) + U_rcut=4*(r_cut**(-12)-r_cut**(-6)) + for atom in range(num-1): + position_relevent=position[atom:,:] + position_other=position_relevent[1:,:] + #pbc rule2 + separation=position_relevent[0,:]-position_other + separation_new=pbc2(separation=separation,L=L) + r_relat=np.sqrt(np.sum(separation_new**2,axis=1)).reshape(separation_new.shape[0],) + LJ=[] + #get out the particles inside the r_limit + for r0 in r_relat: + if r0 <= r_cut: + LJ_num=4*r0**(-12)-4*r0**(-6)-U_rcut-(r0-r_cut)*dU_drcut + LJ.append(LJ_num) + update_LJ[atom,:]=np.sum(np.array(LJ),axis=0) + return np.sum(update_LJ) + +# @numba.njit +def insta_pressure(L,T,position,r_cut,e_scale): + ##This function computes the dimensionless pressure + #Inputs: L -- The size of the simulation cell + # T -- The simulation temperature + # position -- The position of all the particles at this time step + # e_scale -- The energy scale of this particles + #Ouputs: pres_insta -- The instant pressure at this moment + num=position.shape[0] + k_B=1.38064852*10**(-23) + V=L**3 + pres_ideal=num*T*(k_B/e_scale)/V + dU_drcut=24*r_cut**(-7)-48*r_cut**(-13) + pres_virial=np.zeros((num-1,1)) + for atom in range(num-1): + position_relevent=position[atom:,:] + position_other=position_relevent[1:,:] + position_atom=position_relevent[0,:] + #pbc rule 2 + separation=position_atom-position_other + separation_new=pbc2(separation=separation,L=L) + r_relat=np.sqrt(np.sum(separation_new**2,axis=1)).reshape(separation_new.shape[0],) + force=[] + active_r_relat=[] + #get out the particles inside the r_limit + for r0 in r_relat: + if r0 <= r_cut: + #active_r_relat.append(r0) + force_num=-(24*r0**(-7)-48*r0**(-13))+dU_drcut + force.append(force_num) + active_r_relat.append(r0) + #get out the particles inside the r_cut + active_amount=np.array(active_r_relat).shape[0] + rijFij=np.array(active_r_relat).reshape(1,active_amount)@np.array(force).reshape(active_amount,1) + pres_virial[atom,:]=rijFij + pres_insta=pres_ideal+np.sum(pres_virial,axis=0)/(3*V) + return pres_insta + +def cell_to_dict(info,ncore): + # cell_lists = Dict.empty(key_type=types.int64, value_type=float_array) + cell_lists = {} + for i in range(ncore): + cell_lists[i] = np.zeros((1,9)) + for i in range(info.shape[0]): + # atomic coordinates, velocity and acceleration + atom = info[i,0:9].reshape(1,9) + atomID = int(np.floor(i*ncore/info.shape[0])) + 1 + cell_lists[atomID] = np.append(cell_lists[atomID],atom,axis=0) + for i in range(1,ncore): + cell_lists[i] = cell_lists[i][1:,:] + return cell_lists + +def cell_to_obj(info,ncore): + cell_lists = cell_to_dict(info,ncore) + new_cell_list = {} + for i in range(ncore): + if cell_lists[i].shape[0]!=0: + pos = cell_lists[i][:,0:3] # position + vel = cell_lists[i][:,3:6] # velocity + acc = cell_lists[i][:,6:9] # acceleration + spatial_domain_data = spd(pos, vel, acc) + new_cell_list[i] = spatial_domain_data + else: + new_cell_list[i] = spd(np.empty((0,3)),np.empty((0,3)),np.empty((0,3))) + return new_cell_list + +def separate_points_atom(infodict,my_rank): + # since we are using atom-wise decomposition, each processor must know every atomic position + neighbor_spd = None + for i, spd in infodict.items(): + if i!=my_rank: + if neighbor_spd is None: + neighbor_spd = copy.deepcopy(spd) + else: + neighbor_spd.concat(spd) + return infodict[my_rank], neighbor_spd + diff --git a/atom_decompose/utils_parallel.py b/atom_decompose/utils_parallel.py new file mode 100644 index 0000000..e768af6 --- /dev/null +++ b/atom_decompose/utils_parallel.py @@ -0,0 +1,36 @@ +from mpi4py import MPI +# import numba +import utils_spatial_decompose as ut +import numpy as np +import functools +import operator +#@numba.njit() ##This might not be needed +def par_worker_vel_ver_pre(comm,infodict,dt,r_limit,L,my_rank): + vel_Ver(comm,infodict,dt,r_limit,L,my_rank) + +#@numba.njit() +def vel_Ver(comm,infodict,dt,r_limit=2.5,L=6.8,my_rank=0): + # rank = comm.Get_rank() + rank = my_rank + size = comm.Get_size() + ## Get the data for the current spatial domain + my_spd, neighs_spd=ut.separate_points(infodict, rank, size) + # LEAP FROG METHOD + #acceleration at 0 + my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L) + #velocity at dt/2 + my_spd.V=my_spd.V+my_spd.A*(dt/2) + #position at dt + my_spd.P=my_spd.P+my_spd.V*dt + #PBC rule 1 + my_spd.P=ut.pbc1(position=my_spd.P,L=L) + my_spd_send=(rank,my_spd) + comm.barrier() + temp_infodict=comm.allgather(my_spd_send) + # acceleration at dt + my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L) + # velocity at dt + my_spd.V=my_spd.V+my_spd.A*(dt/2) + my_spd_send=(rank,my_spd) + comm.barrier() + return my_spd_send diff --git a/spatial_decompose/MDargon_spatial.py b/spatial_decompose/MDargon_spatial.py index 6dff803..2fafe70 100644 --- a/spatial_decompose/MDargon_spatial.py +++ b/spatial_decompose/MDargon_spatial.py @@ -5,6 +5,13 @@ import utils_spatial_decompose as ut from mpi4py import MPI +# MPI initialize +comm = MPI.COMM_WORLD +rank = comm.Get_rank() +size = comm.Get_size() +print(rank,size) +comm.barrier() + # run params stop_step=1000 k_B=1.38064852*10**(-23) @@ -14,10 +21,10 @@ num_atoms=info_init.shape[0] a_init=np.zeros((num_atoms,3)) -r_c=2.5 +r_c=1.6 L0=6.8 #cube division -subdiv=np.array([2,2,1]) +subdiv=np.array([int(np.sqrt(size)),int(np.sqrt(size)),1]) energy_scale=1.66*10**(-21)#unit: J, Argon sigma=3.4 #unit: Ang, Argon T_dimensional_equal=300#unit K @@ -25,11 +32,7 @@ part_type='LJ' name='argon256' -comm = MPI.COMM_WORLD -rank = comm.Get_rank() -size = comm.Get_size() -print(rank,size) -comm.barrier() + if rank==0: start_time = time.time() @@ -71,12 +74,14 @@ ) temp_infodict=comm.gather(my_spd_send,root=0) if rank == 0: - if step%10==0: + if step%1==0: print('current time step is ', step) temp_infodict=list(filter(None, temp_infodict)) info_temp=dict(temp_infodict) tmp=ut.concatDict(info_temp) info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) + # info[step+1,:,:] = np.round(info[step+1,:,:],4) + info[step+1,:,0:3] = ut.pbc1(info[step+1,:,0:3],L=L0) #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) #calculate and store PE, KE, T_insta, P_insta @@ -91,7 +96,11 @@ end_time = time.time() period = end_time-start_time print(f'Run time is {period:.3f} seconds') - ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, stop_step, False) + PE = np.round(PE,4) + KE = np.round(KE,4) + T_insta = np.round(T_insta,4) + P_insta = np.round(P_insta,4) + ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, size, False) comm.barrier() # 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IMPORTANT: You may need to close and restart your shell after running 'conda init'. +srun: Job step aborted: Waiting up to 302 seconds for job step to finish. +slurmstepd: error: *** JOB 21499407 ON r003 CANCELLED AT 2024-01-03T19:26:44 DUE TO TIME LIMIT *** +slurmstepd: error: *** STEP 21499407.0 ON r003 CANCELLED AT 2024-01-03T19:26:44 DUE TO TIME LIMIT *** diff --git a/spatial_decompose/job.out b/spatial_decompose/job.out index 228d74e..980a382 100644 --- a/spatial_decompose/job.out +++ b/spatial_decompose/job.out @@ -1,107 +1 @@ -/opt/intel/oneapi/intelpython/latest/bin/mpiexec -0 4 -current time step is 0 -current time step is 10 -current time step is 20 -current time step is 30 -current time step is 40 -current time step is 50 -current time step is 60 -current time step is 70 -current time step is 80 -current time step is 90 -current time step is 100 -current time step is 110 -current time step is 120 -current time step is 130 -current time step is 140 -current time step is 150 -current time step is 160 -current time step is 170 -current time step is 180 -current time step is 190 -current time step is 200 -current time step is 210 -current time step is 220 -current time step is 230 -current time step is 240 -current time step is 250 -current time step is 260 -current time step is 270 -current time step is 280 -current time step is 290 -current time step is 300 -current time step is 310 -current time step is 320 -current time step is 330 -current time step is 340 -current time step is 350 -current time step is 360 -current time step is 370 -current time step is 380 -current time step is 390 -current time step is 400 -current time step is 410 -current time step is 420 -current time step is 430 -current time step is 440 -current time step is 450 -current time step is 460 -current time step is 470 -current time step is 480 -current time step is 490 -current time step is 500 -current time step is 510 -current time step is 520 -current time step is 530 -current time step is 540 -current time step is 550 -current time step is 560 -current time step is 570 -current time step is 580 -current time step is 590 -current time step is 600 -current time step is 610 -current time step is 620 -current time step is 630 -current time step is 640 -current time step is 650 -current time step is 660 -current time step is 670 -current time step is 680 -current time step is 690 -current time step is 700 -current time step is 710 -current time step is 720 -current time step is 730 -current time step is 740 -current time step is 750 -current time step is 760 -current time step is 770 -current time step is 780 -current time step is 790 -current time step is 800 -current time step is 810 -current time step is 820 -current time step is 830 -current time step is 840 -current time step is 850 -current time step is 860 -current time step is 870 -current time step is 880 -current time step is 890 -current time step is 900 -current time step is 910 -current time step is 920 -current time step is 930 -current time step is 940 -current time step is 950 -current time step is 960 -current time step is 970 -current time step is 980 -current time step is 990 -Run time is 729.473 seconds -results/argon256iter1000.txt -1 4 -2 4 -3 4 +/opt/intel/oneapi/intelpython/latest/bin/mpirun diff --git a/spatial_decompose/job.sh b/spatial_decompose/job.sh index 5677b59..544b7be 100644 --- a/spatial_decompose/job.sh +++ b/spatial_decompose/job.sh @@ -5,8 +5,8 @@ #SBATCH --mem-per-cpu=2000M #SBATCH -e job.err #SBATCH -o job.out -#SBATCH -t 02:00:00 +#SBATCH -t 00:02:00 -conda activate deepmd-gpu -echo $(which mpiexec) -mpiexec -n 4 python MDargon_spatial.py \ No newline at end of file +conda activate mpi +echo $(which mpirun) +mpiexec -np $SLURM_NTASKS python MDargon_spatial.py \ No newline at end of file diff --git a/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv b/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv new file mode 100644 index 0000000..02939ab --- /dev/null +++ b/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv @@ -0,0 +1,12 @@ +step,KE,PE,T_insta,P_insta +0,391.3016,-413.596,123.0,4.6302 +1,391.1742,-413.0649,122.96,4.6416 +2,390.2459,-411.732,122.6682,4.6643 +3,388.5165,-409.6013,122.1245,4.698 +4,385.9875,-406.673,121.3296,4.7424 +5,382.66,-402.9504,120.2836,4.7978 +6,378.5463,-398.4439,118.9906,4.8639 +7,373.6594,-393.1767,117.4544,4.9401 +8,368.0166,-387.1733,115.6807,5.0261 +9,361.6402,-380.4296,113.6764,5.122 +10,354.5608,-373.0089,111.4511,5.2265 diff --git a/spatial_decompose/results/argon256_Energy_Temp_Pres4core.csv b/spatial_decompose/results/argon256_Energy_Temp_Pres4core.csv new file mode 100644 index 0000000..02939ab --- /dev/null +++ b/spatial_decompose/results/argon256_Energy_Temp_Pres4core.csv @@ -0,0 +1,12 @@ +step,KE,PE,T_insta,P_insta +0,391.3016,-413.596,123.0,4.6302 +1,391.1742,-413.0649,122.96,4.6416 +2,390.2459,-411.732,122.6682,4.6643 +3,388.5165,-409.6013,122.1245,4.698 +4,385.9875,-406.673,121.3296,4.7424 +5,382.66,-402.9504,120.2836,4.7978 +6,378.5463,-398.4439,118.9906,4.8639 +7,373.6594,-393.1767,117.4544,4.9401 +8,368.0166,-387.1733,115.6807,5.0261 +9,361.6402,-380.4296,113.6764,5.122 +10,354.5608,-373.0089,111.4511,5.2265 diff --git a/spatial_decompose/results/argon256core16_summary.txt b/spatial_decompose/results/argon256core16_summary.txt new file mode 100644 index 0000000..6cdd2cb --- /dev/null +++ b/spatial_decompose/results/argon256core16_summary.txt @@ -0,0 +1,6 @@ +Simulation Cell Size(unitless): 6.8 +Simulation Particles Amount: 256 +File Name: argon256 +Simulation Time: 5.574477910995483 +Simulation Step: 10 +Force Cut-off: 1.6 diff --git a/spatial_decompose/results/argon256core4_summary.txt b/spatial_decompose/results/argon256core4_summary.txt new file mode 100644 index 0000000..e39d247 --- /dev/null +++ b/spatial_decompose/results/argon256core4_summary.txt @@ -0,0 +1,6 @@ +Simulation Cell Size(unitless): 6.8 +Simulation Particles Amount: 256 +File Name: argon256 +Simulation Time: 6.41931676864624 +Simulation Step: 10 +Force Cut-off: 1.6 diff --git a/spatial_decompose/results/argon256iter10core16.txt b/spatial_decompose/results/argon256iter10core16.txt new file mode 100644 index 0000000..8f80429 --- /dev/null +++ b/spatial_decompose/results/argon256iter10core16.txt @@ -0,0 +1,256 @@ +0.801900 0.761900 0.022400 1.362800 -0.571900 1.024600 -8.927200 0.727600 -12.516300 +0.005800 0.783500 2.310200 0.208400 0.465300 -0.485000 -9.247800 -5.108600 4.446600 +0.768100 0.792200 1.559000 -0.282200 0.900500 0.572300 -1.306200 -5.448100 -4.061200 +0.764600 0.772500 3.099100 -0.444600 -0.035800 0.228600 -1.455200 1.526900 -3.169900 +0.001200 0.003900 4.666100 0.000400 0.152100 1.207000 -6.829100 -4.528600 -7.047600 +0.755900 0.013000 5.402900 -0.863500 0.587900 -0.512800 2.585200 -6.279000 9.339400 +0.784200 0.814800 4.649000 0.506600 1.979700 0.371200 -4.646900 -12.776800 -1.228500 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3.871600 3.871700 -0.702900 0.985400 1.018000 0.393700 -0.507500 -1.261600 +5.422900 3.871400 3.094100 2.055600 0.941400 -0.015500 7.400000 -0.426700 0.554400 +4.646800 3.868100 5.422100 1.398900 0.121700 1.842900 -1.215600 0.656300 7.843900 +5.417500 3.867600 4.639100 0.700800 -0.009400 -0.518200 8.310300 -0.083300 0.138300 +4.636800 4.641400 6.799600 -1.078900 0.056800 -0.109700 0.556800 0.334600 -8.074800 +4.633600 5.419700 0.767900 -1.885900 1.255400 -1.420500 0.664700 7.825000 1.142100 +5.418500 4.647700 0.778400 0.968400 1.625100 1.218000 7.712600 -0.508300 -1.028900 +5.413700 5.418500 0.000400 -0.232000 0.930100 0.075700 3.803900 3.806000 -3.928500 +4.646100 4.645000 1.545100 1.227200 0.947100 -0.501400 -0.934700 -0.731600 0.786500 +4.637500 5.417400 2.324200 -0.916000 0.684600 0.893500 0.510000 7.758600 -0.082500 +5.417100 4.634600 2.326000 0.590900 -1.656700 1.331700 7.786500 0.603900 -0.505200 +5.417200 5.412300 1.552700 0.630500 -0.589400 1.396500 5.771700 6.403900 -0.031400 +4.632400 4.633500 3.088500 -2.211800 -1.924100 -1.422300 0.581800 0.325300 1.014400 +4.643400 5.408500 3.867300 0.536500 -1.532100 -0.077200 -0.960100 8.008600 0.020600 +5.421500 4.648400 3.869600 1.723400 1.793200 0.497700 7.784800 -1.247100 -0.670800 +5.411600 5.413200 3.093700 -0.772200 -0.368500 -0.097700 6.026200 5.988500 -0.206900 +4.646400 4.637800 4.640800 1.285400 -0.856500 -0.104400 -1.486300 -0.011500 0.091900 +4.639400 5.409700 5.408900 -0.462000 -1.241100 -1.441200 -0.253400 6.494800 6.236400 +5.416600 4.642200 5.413300 0.480300 0.264300 -0.346900 6.395300 -0.220200 6.194800 +5.413300 5.414500 4.640000 -0.347900 -0.056900 -0.278000 6.407600 6.501500 0.065700 diff --git a/spatial_decompose/temp.txt b/spatial_decompose/temp.txt new file mode 100644 index 0000000..b618e9a --- /dev/null +++ b/spatial_decompose/temp.txt @@ -0,0 +1,20 @@ +4core +update accel [-8.45424897 0.44704291 -0.33678861] +[[-1.45904247e-02 -2.29175846e+00 2.27839159e+00] + [-1.86997900e-02 2.35280556e+00 2.36481349e+00] + [-2.12388218e+00 2.09121071e+00 1.86267859e-03] + [-2.68427912e-02 2.63770860e+00 -2.64739033e+00] + [-2.10905225e+00 -1.22518734e-02 2.09175120e+00] + [-2.13116430e+00 -1.42712217e-02 -2.11631902e+00] + [-2.01381352e+00 -2.00512265e+00 -6.49800616e-03] + [-1.62037165e-02 -2.31127776e+00 -2.30340022e+00]] [1.09461502 1.09352185 1.09733541 1.08949982 1.09744812 1.09708215 + 1.09889725 1.0942828 ] + + +16core +update accel [-6.2848242 -6.63468197 -0.05607445] +[[-0.01459042 -2.29175846 2.27839159] + [-2.10905225 -0.01225187 2.0917512 ] + [-2.1311643 -0.01427122 -2.11631902] + [-2.01381352 -2.00512265 -0.00649801] + [-0.01620372 -2.31127776 -2.30340022]] [1.09461502 1.09744812 1.09708215 1.09889725 1.0942828 ] \ No newline at end of file diff --git a/spatial_decompose/utils_parallel.py b/spatial_decompose/utils_parallel.py index e768af6..d222460 100644 --- a/spatial_decompose/utils_parallel.py +++ b/spatial_decompose/utils_parallel.py @@ -17,20 +17,21 @@ def vel_Ver(comm,infodict,dt,r_limit=2.5,L=6.8,my_rank=0): my_spd, neighs_spd=ut.separate_points(infodict, rank, size) # LEAP FROG METHOD #acceleration at 0 - my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L) + my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L,rank=my_rank) #velocity at dt/2 - my_spd.V=my_spd.V+my_spd.A*(dt/2) + # my_spd.V=my_spd.V+my_spd.A*(dt/2) + my_spd.V=my_spd.V+my_spd.A*(dt) #position at dt my_spd.P=my_spd.P+my_spd.V*dt #PBC rule 1 my_spd.P=ut.pbc1(position=my_spd.P,L=L) my_spd_send=(rank,my_spd) comm.barrier() - temp_infodict=comm.allgather(my_spd_send) - # acceleration at dt - my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L) - # velocity at dt - my_spd.V=my_spd.V+my_spd.A*(dt/2) - my_spd_send=(rank,my_spd) - comm.barrier() + # temp_infodict=comm.allgather(my_spd_send) + # # acceleration at dt + # my_spd.A=ut.LJ_accel(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_limit,L=L,rank=my_rank) + # # velocity at dt + # my_spd.V=my_spd.V+my_spd.A*(dt/2) + # my_spd_send=(rank,my_spd) + # comm.barrier() return my_spd_send diff --git a/spatial_decompose/utils_spatial_decompose.py b/spatial_decompose/utils_spatial_decompose.py index 41c6efa..9437a26 100644 --- a/spatial_decompose/utils_spatial_decompose.py +++ b/spatial_decompose/utils_spatial_decompose.py @@ -42,7 +42,8 @@ def pbc1(position,L): position_axis = position_ind[j] if position_axis < 0: position_axis_new=position_axis+L - elif position_axis > L: + elif position_axis >= L: + print(position_axis) position_axis_new=position_axis-L else: position_axis_new=position_axis @@ -65,7 +66,7 @@ def pbc2(separation,L): separation_axis = separation_ind[j] if separation_axis < -L/2: separation_axis_new=separation_axis+L - elif separation_axis > L/2: + elif separation_axis >= L/2: separation_axis_new=separation_axis-L else: separation_axis_new=separation_axis @@ -184,6 +185,7 @@ def cell_to_dict(info,nx,ny,nz,L): xinterval=L/nx yinterval=L/ny zinterval=L/nz + # print('interval ', xinterval, yinterval) #cell_lists={} for i in range(nx*ny*nz): cell_dict[i]= np.zeros((1,9)) @@ -192,7 +194,10 @@ def cell_to_dict(info,nx,ny,nz,L): #check extra one!!! #if statements !!!!!!! #check later - atomID=int(((np.floor(atom[:,0]/xinterval)+(np.floor(atom[:,1]/yinterval))*ny)+(np.floor(atom[:,2]/zinterval))*(nx*ny))[0]) + # atomID=int(((np.floor(atom[:,0]/xinterval)+(np.floor(atom[:,1]/yinterval))*ny)+(np.floor(atom[:,2]/zinterval))*(nx*ny))[0]) + atomID=int(((np.floor(atom[:,0]/xinterval)+(np.floor(atom[:,1]/yinterval))*ny))[0]) + if atomID>15: + print(atomID,atom, atom[:,0][0]==L) cell_dict[atomID]=np.append(cell_dict[atomID],atom,axis=0) for i in range(nx*ny*nz): cell_dict[i]=cell_dict[i][1:,:] @@ -226,7 +231,7 @@ def separate_points(infodict, my_rank, nproc): # Processor matrix n*n*1 (for comparison with force decomposition) axis = np.sqrt(nproc) # Here we need to be careful about only copying the neighboring subcube - x,y,z = my_rank / axis, my_rank % axis, 0 + x,y,z = my_rank % axis, my_rank / axis, 0 x,y,z = int(np.floor(x)), int(np.floor(y)), int(np.floor(z)) x_mesh,y_mesh = np.meshgrid(np.linspace(x-1,x+1,3),np.linspace(y-1,y+1,3)) neighbor_xy = np.column_stack((x_mesh.ravel(),y_mesh.ravel())) @@ -240,13 +245,30 @@ def separate_points(infodict, my_rank, nproc): else: neighbor_rank = np.zeros(9) for t,xy in enumerate(neighbor_xy): - for i in xy: - if i<0: - i = i + axis - elif i == axis: - i = i - axis + xy_old = xy.copy() + if xy[0]<0: + xy[0] = xy[0] + axis + if xy[0]==axis: + xy[0] = xy[0] - axis + # elif xy[0]==axis and xy[1]=axis-1: + # xy[0] = xy[0] - axis + # xy[1] = 0 + if xy[1]<0: + xy[1] = xy[1] + axis + if xy[1] == axis: + xy[1] = xy[1] - axis + # xy[0] = xy[0] + # print(xy_old,xy) + # for i in xy: + # if i<0: + # i = i + axis + # elif i == axis: + # i = i - axis neighbor_rank[t] = (xy[0] + xy[1]*axis) - # print('neighboring ',my_rank, neighbor_rank) + # print('neighboring ',my_rank, (x,y), neighbor_rank) # copy the info in neighboring ranks for i, spd in infodict.items(): @@ -268,7 +290,7 @@ def concatDict(infodict): return wholeDict #@numba.njit() -def LJ_accel(position,neighb_x_0,r_cut,L): +def LJ_accel(position,neighb_x_0,r_cut,L, rank): subcube_atoms=position.shape[0] #careful kind of confusing position=np.concatenate((position,neighb_x_0),0) @@ -284,6 +306,7 @@ def LJ_accel(position,neighb_x_0,r_cut,L): r_relat=np.sqrt(np.sum(separation_new**2,axis=1)) #get out the particles inside the r_cut accel=np.zeros((r_relat.shape[0],3)) + flag = 0 for i, r0 in enumerate(r_relat): if r0 <= r_cut: separation_active_num=separation_new[i,:] @@ -291,17 +314,23 @@ def LJ_accel(position,neighb_x_0,r_cut,L): scalar_part=48*r0**(-13)-24*r0**(-7)-dU_drcut accel_num=vector_part*scalar_part accel[i,:]=accel_num + # if np.abs(position_atom[0]-4.641496)<0.001 and np.abs(position_atom[1]-3.092705)<0.001 and np.abs(position_atom[2]-3.090466)<0.001: + # flag = 1 + # print(position_atom, accel_num, r0) update_accel[atom,:]=np.sum(accel,axis=0) + # if np.abs(update_accel[atom,:][0]+6.2848242)<1e-4: + # print('update accel',update_accel[atom,:]) + # print(accel[accel.any(axis=1)],r_relat[accel.any(axis=1)]) return update_accel.reshape(subcube_atoms,3) -def data_saver(info, PE, KE, T_insta, P_insta, L, num_atoms,part_type,name,period,stop_step, r_c, iterations_int=1000, make_directory=True): - iterations=str(iterations_int) +def data_saver(info, PE, KE, T_insta, P_insta, L, num_atoms,part_type,name,period,stop_step, r_c, ncore = 8, make_directory=True): + iterations=str(stop_step) if make_directory == True: os.mkdir('results') # path_to_file_xyz="results/"+name+"position_last"+iterations+"stps"+".xyz" - path_to_file_xyz = "results/"+name+"iter"+iterations+'.txt' - path_to_file_other = "results/"+name+"_Energy_Temp_Pres"+".csv" - path_to_file_summary = "results/"+name+"_summary"+".txt" + path_to_file_xyz = "results/"+name+"iter"+iterations+'core'+str(ncore)+'.txt' + path_to_file_other = "results/"+name+"_Energy_Temp_Pres"+str(ncore)+'core'+".csv" + path_to_file_summary = "results/"+name+'core'+str(ncore)+"_summary"+".txt" p= open(path_to_file_xyz,"w") s= open(path_to_file_summary,'w') @@ -316,13 +345,15 @@ def data_saver(info, PE, KE, T_insta, P_insta, L, num_atoms,part_type,name,perio #writing xyz file comment = 'This is the position of the system of the final step' - print(path_to_file_xyz) + # print(path_to_file_xyz) # for atoms in info[-int(iterations):,:,:]: # p.write("%s\n" % str(num_atoms)) # p.write("%s\n" % comment) # for i in range(num_atoms): # p.write("\t%s\n" % str(info[:])) - np.savetxt(path_to_file_xyz,info[-1,:,:],fmt='%.6f') + # output = info[-1,:,:][np.argsort(info[-1,:,0])] + output = info[-1,:,:] + np.savetxt(path_to_file_xyz,output,fmt='%.6f') #writing other file other_dict={} From 52cc3fd45ab0ef9667486d964c720d08e73c6159 Mon Sep 17 00:00:00 2001 From: Hancheng Zhao Date: Thu, 4 Jan 2024 13:51:49 -0500 Subject: [PATCH 5/9] solved problem with mpirun, spatial decomp now working --- spatial_decompose/MDargon_spatial.py | 2 +- .../LJ_SpatialDecomp.cpython-310.pyc | Bin 1905 -> 1870 bytes .../utils_parallel.cpython-310.pyc | Bin 1268 -> 976 bytes .../utils_spatial_decompose.cpython-310.pyc | Bin 9031 -> 8567 bytes spatial_decompose/job.err | 3 - spatial_decompose/job.out | 101 ++ spatial_decompose/job.sh | 9 +- .../argon256_Energy_Temp_Pres16core.csv | 1010 ++++++++++++++++- .../argon256_Energy_Temp_Pres4core.csv | 1010 ++++++++++++++++- .../results/argon256iter1000core16.txt | 256 +++++ ...txt => argon256iter1000core16_summary.txt} | 4 +- .../results/argon256iter1000core4.txt | 256 +++++ .../results/argon256iter1000core4_summary.txt | 6 + spatial_decompose/utils_spatial_decompose.py | 2 +- 14 files changed, 2628 insertions(+), 31 deletions(-) create mode 100644 spatial_decompose/results/argon256iter1000core16.txt rename spatial_decompose/results/{argon256core4_summary.txt => argon256iter1000core16_summary.txt} (65%) create mode 100644 spatial_decompose/results/argon256iter1000core4.txt create mode 100644 spatial_decompose/results/argon256iter1000core4_summary.txt diff --git a/spatial_decompose/MDargon_spatial.py b/spatial_decompose/MDargon_spatial.py index 2fafe70..5d6875a 100644 --- a/spatial_decompose/MDargon_spatial.py +++ b/spatial_decompose/MDargon_spatial.py @@ -74,7 +74,7 @@ ) temp_infodict=comm.gather(my_spd_send,root=0) if rank == 0: - if step%1==0: + if step%20==0: print('current time step is ', step) temp_infodict=list(filter(None, temp_infodict)) info_temp=dict(temp_infodict) diff --git a/spatial_decompose/__pycache__/LJ_SpatialDecomp.cpython-310.pyc b/spatial_decompose/__pycache__/LJ_SpatialDecomp.cpython-310.pyc index 46e8e2366741d14f9ee85df511057376d1e1ab8c..1721536a7305d3a1450f8523708dd3b5d9110613 100644 GIT binary patch delta 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IMPORTANT: You may need to close and restart your shell after running 'conda init'. -srun: Job step aborted: Waiting up to 302 seconds for job step to finish. -slurmstepd: error: *** JOB 21499407 ON r003 CANCELLED AT 2024-01-03T19:26:44 DUE TO TIME LIMIT *** -slurmstepd: error: *** STEP 21499407.0 ON r003 CANCELLED AT 2024-01-03T19:26:44 DUE TO TIME LIMIT *** diff --git a/spatial_decompose/job.out b/spatial_decompose/job.out index 980a382..599a033 100644 --- a/spatial_decompose/job.out +++ b/spatial_decompose/job.out @@ -1 +1,102 @@ /opt/intel/oneapi/intelpython/latest/bin/mpirun +1 16 +3 16 +4 16 +5 16 +6 16 +7 16 +8 16 +9 16 +11 16 +12 16 +13 16 +14 16 +15 16 +0 16 +2 16 +10 16 +current time step is 0 +current time step is 20 +current time step is 40 +current time step is 60 +current time step is 80 +6.800088657224866 +current time step is 100 +current time step is 120 +current time step is 140 +current time step is 160 +current time step is 180 +current time step is 200 +current time step is 220 +6.800887957082665 +6.800481721319657 +6.801291421279879 +current time step is 240 +current time step is 260 +current time step is 280 +current time step is 300 +6.80107135517086 +current time step is 320 +current time step is 340 +current time step is 360 +current time step is 380 +6.800504763517787 +current time step is 400 +current time step is 420 +current time step is 440 +6.802346649248434 +6.801138516114344 +6.802031021387378 +current time step is 460 +6.800763838812504 +current time step is 480 +6.80089179163358 +6.802358924955001 +current time step is 500 +6.800859721949978 +current time step is 520 +6.801626610851169 +6.802377691457664 +current time step is 540 +current time step is 560 +6.8010504448147255 +6.803229807623406 +current time step is 580 +6.800451042061884 +6.8010979179850555 +current time step is 600 +6.8008727928451105 +current time step is 620 +current time step is 640 +6.802398062547351 +6.800161513604769 +current time step is 660 +current time step is 680 +6.800895694974772 +6.802513429734919 +current time step is 700 +current time step is 720 +current time step is 740 +6.800686842176662 +current time step is 760 +6.801545423101174 +current time step is 780 +current time step is 800 +6.800557966697346 +6.801625648105528 +current time step is 820 +6.800409953971007 +current time step is 840 +current time step is 860 +current time step is 880 +6.802851576849863 +current time step is 900 +current time step is 920 +6.800308721184406 +6.803093891584433 +current time step is 940 +6.800466916213642 +6.804489156110476 +current time step is 960 +current time step is 980 +Run time is 488.412 seconds diff --git a/spatial_decompose/job.sh b/spatial_decompose/job.sh index 544b7be..816ac6f 100644 --- a/spatial_decompose/job.sh +++ b/spatial_decompose/job.sh @@ -1,12 +1,13 @@ #!/bin/bash #SBATCH -N 1 -#SBATCH -n 4 +#SBATCH -n 16 #SBATCH -p RM-small #SBATCH --mem-per-cpu=2000M #SBATCH -e job.err #SBATCH -o job.out -#SBATCH -t 00:02:00 +#SBATCH -t 01:00:00 -conda activate mpi +conda activate dpgpu +# module load openmpi/4.0.5-gcc10.2.0 echo $(which mpirun) -mpiexec -np $SLURM_NTASKS python MDargon_spatial.py \ No newline at end of file +~/.conda/envs/dpgpu/bin/mpirun -np $SLURM_NTASKS python MDargon_spatial.py \ No newline at end of file diff --git a/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv b/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv index 02939ab..49ad0d8 100644 --- a/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv +++ b/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv @@ -1,12 +1,1002 @@ step,KE,PE,T_insta,P_insta 0,391.3016,-413.596,123.0,4.6302 -1,391.1742,-413.0649,122.96,4.6416 -2,390.2459,-411.732,122.6682,4.6643 -3,388.5165,-409.6013,122.1245,4.698 -4,385.9875,-406.673,121.3296,4.7424 -5,382.66,-402.9504,120.2836,4.7978 -6,378.5463,-398.4439,118.9906,4.8639 -7,373.6594,-393.1767,117.4544,4.9401 -8,368.0166,-387.1733,115.6807,5.0261 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-1.340408 1.924213 +5.970013 4.695155 5.721996 0.322910 -0.357412 -0.453712 -2.371453 17.587561 0.870424 +5.821344 5.609640 5.037978 1.311789 -1.233023 0.108565 3.973692 -3.274903 -5.612499 diff --git a/spatial_decompose/results/argon256iter1000core4_summary.txt b/spatial_decompose/results/argon256iter1000core4_summary.txt new file mode 100644 index 0000000..1a69b69 --- /dev/null +++ b/spatial_decompose/results/argon256iter1000core4_summary.txt @@ -0,0 +1,6 @@ +Simulation Cell Size(unitless): 6.8 +Simulation Particles Amount: 256 +File Name: argon256 +Simulation Time: 569.6633203029633 +Simulation Step: 1000 +Force Cut-off: 1.6 diff --git a/spatial_decompose/utils_spatial_decompose.py b/spatial_decompose/utils_spatial_decompose.py index 9437a26..a9b5085 100644 --- a/spatial_decompose/utils_spatial_decompose.py +++ b/spatial_decompose/utils_spatial_decompose.py @@ -330,7 +330,7 @@ def data_saver(info, PE, KE, T_insta, P_insta, L, num_atoms,part_type,name,perio # path_to_file_xyz="results/"+name+"position_last"+iterations+"stps"+".xyz" path_to_file_xyz = "results/"+name+"iter"+iterations+'core'+str(ncore)+'.txt' path_to_file_other = "results/"+name+"_Energy_Temp_Pres"+str(ncore)+'core'+".csv" - path_to_file_summary = "results/"+name+'core'+str(ncore)+"_summary"+".txt" + path_to_file_summary = "results/"+name+"iter"+iterations+'core'+str(ncore)+"_summary"+".txt" p= open(path_to_file_xyz,"w") s= open(path_to_file_summary,'w') From f3dbd74c3ddb1a571753ddf0025c6892599f0a8f Mon Sep 17 00:00:00 2001 From: Hancheng Zhao Date: Thu, 4 Jan 2024 17:37:56 -0500 Subject: [PATCH 6/9] add serial --- spatial_decompose/MDargon_serial.py | 146 +++ spatial_decompose/MDargon_spatial.py | 30 +- .../utils_parallel.cpython-310.pyc | Bin 976 -> 976 bytes .../utils_spatial_decompose.cpython-310.pyc | Bin 8567 -> 8575 bytes spatial_decompose/job.out | 81 +- spatial_decompose/job.sh | 5 +- .../results_before_PE_parallel/MDargon.py | 122 ++ .../argon256_Energy_Temp_Pres.csv | 0 .../argon256_Energy_Temp_Pres16core.csv | 0 .../argon256_Energy_Temp_Pres1core.csv} | 0 .../argon256_Energy_Temp_Pres4core.csv | 1002 +++++++++++++++++ .../argon256_summary.txt | 0 .../argon256core16_summary.txt | 0 .../argon256iter1.txt | 0 .../argon256iter1000.txt | 0 .../argon256iter1000core1.txt | 256 +++++ .../argon256iter1000core16.txt | 0 .../argon256iter1000core16_summary.txt | 0 .../argon256iter1000core1_summary.txt | 6 + .../argon256iter1000core4.txt | 0 .../argon256iter1000core4_summary.txt | 0 .../argon256iter10core16.txt | 0 .../argon256iter10core4.txt | 0 .../argon256iter1core1.txt | 256 +++++ .../argon256iter1core1_summary.txt | 6 + .../argon256iter1core4.txt | 0 .../argon256iter2core16.txt | 0 .../argon256iter2core4.txt | 0 spatial_decompose/utils_spatial_decompose.py | 2 +- 29 files changed, 1853 insertions(+), 59 deletions(-) create mode 100644 spatial_decompose/MDargon_serial.py create mode 100644 spatial_decompose/results_before_PE_parallel/MDargon.py rename spatial_decompose/{results => results_before_PE_parallel}/argon256_Energy_Temp_Pres.csv (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256_Energy_Temp_Pres16core.csv (100%) rename spatial_decompose/{results/argon256_Energy_Temp_Pres4core.csv => results_before_PE_parallel/argon256_Energy_Temp_Pres1core.csv} (100%) create mode 100644 spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres4core.csv rename spatial_decompose/{results => results_before_PE_parallel}/argon256_summary.txt (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256core16_summary.txt (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter1.txt (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter1000.txt (100%) create mode 100644 spatial_decompose/results_before_PE_parallel/argon256iter1000core1.txt rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter1000core16.txt (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter1000core16_summary.txt (100%) create mode 100644 spatial_decompose/results_before_PE_parallel/argon256iter1000core1_summary.txt rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter1000core4.txt (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter1000core4_summary.txt (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter10core16.txt (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter10core4.txt (100%) create mode 100644 spatial_decompose/results_before_PE_parallel/argon256iter1core1.txt create mode 100644 spatial_decompose/results_before_PE_parallel/argon256iter1core1_summary.txt rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter1core4.txt (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter2core16.txt (100%) rename spatial_decompose/{results => results_before_PE_parallel}/argon256iter2core4.txt (100%) diff --git a/spatial_decompose/MDargon_serial.py b/spatial_decompose/MDargon_serial.py new file mode 100644 index 0000000..7597818 --- /dev/null +++ b/spatial_decompose/MDargon_serial.py @@ -0,0 +1,146 @@ +import numpy as np +import time +import copy +from LJ_SpatialDecomp import * +import utils_spatial_decompose as ut +from mpi4py import MPI + + +def LJ_acc(position,r_cut,L, rank): + subcube_atoms=position.shape[0] + #careful kind of confusing + num=position.shape[0] + update_accel=np.zeros((subcube_atoms,3)) + dU_drcut=48*r_cut**(-13)-24*r_cut**(-7) + #for loop is only of subcube we are interested in but we have to account for ALL distance! + for atom in range(subcube_atoms): + position_other=np.concatenate((position[0:atom,:],position[atom+1:num+1,:]),axis=0) + position_atom=position[atom] + separation=position_atom-position_other + separation_new=ut.pbc2(separation=separation,L=L) + r_relat=np.sqrt(np.sum(separation_new**2,axis=1)) + #get out the particles inside the r_cut + accel=np.zeros((r_relat.shape[0],3)) + flag = 0 + for i, r0 in enumerate(r_relat): + if r0 <= r_cut and r0!=0: + separation_active_num=separation_new[i,:] + vector_part=separation_active_num*(1/r0) + scalar_part=48*r0**(-13)-24*r0**(-7)-dU_drcut + accel_num=vector_part*scalar_part + accel[i,:]=accel_num + # if np.abs(position_atom[0]-4.641496)<0.001 and np.abs(position_atom[1]-3.092705)<0.001 and np.abs(position_atom[2]-3.090466)<0.001: + # flag = 1 + # print(position_atom, accel_num, r0) + update_accel[atom,:]=np.sum(accel,axis=0) + # if np.abs(update_accel[atom,:][0]+6.2848242)<1e-4: + # print('update accel',update_accel[atom,:]) + # print(accel[accel.any(axis=1)],r_relat[a + return update_accel.reshape(subcube_atoms,3) + +# MPI initialize +comm = MPI.COMM_WORLD +rank = comm.Get_rank() +size = comm.Get_size() +print(rank,size) +comm.barrier() + +# run params +stop_step=1000 +k_B=1.38064852*10**(-23) +dt=0.002 +file_name='../data/initial_position_LJ_argon256.txt' +info_init=np.loadtxt(file_name) +num_atoms=info_init.shape[0] + +a_init=np.zeros((num_atoms,3)) +r_c=1.6 +L0=6.8 +#cube division +subdiv=np.array([int(np.sqrt(size)),int(np.sqrt(size)),1]) +energy_scale=1.66*10**(-21)#unit: J, Argon +sigma=3.4 #unit: Ang, Argon +T_dimensional_equal=300#unit K +T_equal=T_dimensional_equal*k_B/energy_scale +part_type='LJ' +name='argon256' + +# if rank==0: +start_time = time.time() +# # initialize +k_B=1.38064852*10**(-23) +size_sim=info_init.shape[0] +# x_dot_init=ut.random_vel_generator(size_sim,T_equal,energy_scale) +#initialize PE, KE, T_insta, P_insta, Momentum +PE=np.zeros((stop_step+1,1)) +KE=np.zeros((stop_step+1,1)) +T_insta=np.zeros((stop_step+1,1)) +P_insta=np.zeros((stop_step+1,1)) +#initialize the info matrix +info=np.zeros((stop_step+1,size_sim,9)) +# info[0,:,:]=np.concatenate((position_init,x_dot_init,a_init),axis=1) +info[0,:,:] = info_init +# np.savetxt('../data/init.txt',info[0,:,:],fmt='%.6f') +infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L0) +#zero step value +PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_c,L=L0) +KE[0,:]=ut.Kin_Eng(info[0,:,3:6]) +T_insta[0,:]=2*KE[0,:]*energy_scale/(3*(size_sim-1)*k_B) #k +P_insta[0,:]=ut.insta_pressure(L0,T_insta[0],info[0,:,0:3],r_c,energy_scale) #unitless + +# Run MD +for step in range(stop_step): + # neighboring atoms + neighb_spd = infotodic[0] + my_spd = infotodic[0] + my_spd.A = ut.LJ_accel(position=my_spd.P,neighb_x_0=neighb_spd.P,r_cut=r_c,L=L0,rank=0)/2.0 + my_spd.V=my_spd.V+my_spd.A*(dt) + my_spd.P=my_spd.P+my_spd.V*dt + my_spd.P=ut.pbc1(position=my_spd.P,L=L0) + if step%20==0: + print('current time step is ', step) + temp_infodict = (0,my_spd) + temp_infodict=list(filter(None, temp_infodict)) + temp_infodict = [(0,my_spd)] + info_temp=dict(temp_infodict) + # print(info_temp) + tmp=ut.concatDict(info_temp) + info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) + # info[step+1,:,:] = np.round(info[step+1,:,:],4) + info[step+1,:,0:3] = ut.pbc1(info[step+1,:,0:3],L=L0) + #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES + infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) + + #calculate and store PE, KE, T_insta, P_insta in parallel + PE[step+1,:]=ut.LJ_potent_nondimen(info[step+1,:,0:3],r_cut=r_c,L=L0) + KE[step+1,:]=ut.Kin_Eng(info[step+1,:,3:6]) + T_insta[step+1,:]=2*KE[step+1,:]*energy_scale/(3*(size_sim-1)*k_B) #k + P_insta[step+1,:]=ut.insta_pressure(L0,T_insta[step+1],info[step+1,:,0:3],r_c,energy_scale) #unitless + + +end_time = time.time() +period = end_time-start_time +print(f'Run time is {period:.3f} seconds') +PE = np.round(PE,4) +KE = np.round(KE,4) +T_insta = np.round(T_insta,4) +P_insta = np.round(P_insta,4) +ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, size, False) + +# if rank==0: +# start_time=time.time() +# info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, +# position_init=position_init, +# dt=dt, +# stop_step=stop_step, +# accel_init=a_init, +# r_cut=2.8, +# L=L0, +# T_eq=T_equal, +# e_scale=energy_scale, +# sig=sigma) +# end_time=time.time() +# period = end_time-start_time +# print("For this {} steps operation (dt={}) with r_cut = {} and L = {}, it took:".format(stop_step,dt,r_c,L0),end_time-start_time,'s') +# ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, 1000, False) +# else: diff --git a/spatial_decompose/MDargon_spatial.py b/spatial_decompose/MDargon_spatial.py index 5d6875a..94cddcd 100644 --- a/spatial_decompose/MDargon_spatial.py +++ b/spatial_decompose/MDargon_spatial.py @@ -59,7 +59,7 @@ else: infotodic = None # info = None -comm.barrier() +# comm.barrier() infotodic = comm.bcast(infotodic, root = 0) # Run MD @@ -72,7 +72,20 @@ L=L0, my_rank=rank ) + # apply periodic boundary condition + my_spd_send[1].P = ut.pbc1(my_spd_send[1].P,L=L0) + #calculate and store PE, KE, T_insta, P_insta in parallel + PE_single = ut.LJ_potent_nondimen(my_spd_send[1].P,r_cut=r_c,L=L0) + KE_single = ut.Kin_Eng(my_spd_send[1].V) + T_single = 2*KE_single*energy_scale/(3*(my_spd_send[1].P.shape[0]-1)*k_B) #k + # P_single = ut.insta_pressure(L0,) + + # gather temp_infodict=comm.gather(my_spd_send,root=0) + comm.reduce([PE_single,MPI.FLOAT],None,op=MPI.SUM,root=0) + comm.reduce([KE_single,MPI.FLOAT],None,op=MPI.SUM,root=0) + comm.reduce([T_single,MPI.FLOAT],None,op=MPI.SUM,root=0) + if rank == 0: if step%20==0: print('current time step is ', step) @@ -81,15 +94,16 @@ tmp=ut.concatDict(info_temp) info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) # info[step+1,:,:] = np.round(info[step+1,:,:],4) - info[step+1,:,0:3] = ut.pbc1(info[step+1,:,0:3],L=L0) + # info[step+1,:,0:3] = ut.pbc1(info[step+1,:,0:3],L=L0) #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) - #calculate and store PE, KE, T_insta, P_insta - PE[step+1,:]=ut.LJ_potent_nondimen(info[step+1,:,0:3],r_cut=r_c,L=L0) - KE[step+1,:]=ut.Kin_Eng(info[step+1,:,3:6]) - T_insta[step+1,:]=2*KE[step+1,:]*energy_scale/(3*(size_sim-1)*k_B) #k - P_insta[step+1,:]=ut.insta_pressure(L0,T_insta[step+1],info[step+1,:,0:3],r_c,energy_scale) #unitless - comm.barrier() + + #calculate and store PE, KE, T_insta, P_insta in parallel + PE[step+1,:]=PE_single + KE[step+1,:]=KE_single + T_insta[step+1,:]=T_single/size + # P_insta[step+1,:]=ut.insta_pressure(L0,T_insta[step+1],info[step+1,:,0:3],r_c,energy_scale) #unitless + # comm.barrier() infotodic=comm.bcast(infotodic,root=0) if rank == 0: diff --git a/spatial_decompose/__pycache__/utils_parallel.cpython-310.pyc b/spatial_decompose/__pycache__/utils_parallel.cpython-310.pyc index 08aaa29fed4ff4c71e0694eb7d114fdf592dfa2e..ee3f1aa17a4d8d310d97f7e4c75b688bdc18d25f 100644 GIT binary patch delta 20 acmcb>eu14kpO=@50SLnWP20$Qloeu14kpO=@50SIPuOx?(Rlo$iX*<=>U zFvjl5(UKFzO=6g81#5+Bgld?w8H<+H2&FJ)GZ!tJ{9E!B7; z0BNQM85SOvqTJ1|r57*@lmRU(Dg_bcAfjUPYdy0TNMc1&MhniN!??lb0sz-}IOYHV delta 197 zcmezG^xcU!pO=@50SI2XPD_p4$m=dHc#A!^GQKD=FFT4gub?PDIcjsN_&i3&yvZz* zVT|pQqa`Qu8^kcx3f2nM2-PrUGZrnH%q;baF>3NVsgEKYi~@{2j53TMnyEpCg@>gm zXY*(21i_@% diff --git a/spatial_decompose/job.out b/spatial_decompose/job.out index 599a033..7b5f150 100644 --- a/spatial_decompose/job.out +++ b/spatial_decompose/job.out @@ -1,20 +1,5 @@ /opt/intel/oneapi/intelpython/latest/bin/mpirun -1 16 -3 16 -4 16 -5 16 -6 16 -7 16 -8 16 -9 16 -11 16 -12 16 -13 16 -14 16 -15 16 -0 16 -2 16 -10 16 +0 1 current time step is 0 current time step is 20 current time step is 40 @@ -29,74 +14,74 @@ current time step is 180 current time step is 200 current time step is 220 6.800887957082665 -6.800481721319657 -6.801291421279879 +6.800481721319658 +6.801291421279881 current time step is 240 current time step is 260 current time step is 280 current time step is 300 -6.80107135517086 +6.801071355170859 current time step is 320 current time step is 340 current time step is 360 current time step is 380 -6.800504763517787 +6.800504763517788 current time step is 400 current time step is 420 current time step is 440 -6.802346649248434 -6.801138516114344 -6.802031021387378 +6.802346649248438 +6.801138516114347 +6.802031021387377 current time step is 460 -6.800763838812504 +6.800763838812505 current time step is 480 -6.80089179163358 +6.800891791633579 6.802358924955001 current time step is 500 -6.800859721949978 +6.800859721949975 current time step is 520 -6.801626610851169 -6.802377691457664 +6.801626610851167 +6.802377691457667 current time step is 540 current time step is 560 -6.8010504448147255 -6.803229807623406 +6.801050444814723 +6.803229807623386 current time step is 580 -6.800451042061884 -6.8010979179850555 +6.8004510420618836 +6.801097917985061 current time step is 600 -6.8008727928451105 +6.800872792845088 current time step is 620 current time step is 640 -6.802398062547351 -6.800161513604769 +6.802398062547355 +6.800161513604764 current time step is 660 current time step is 680 -6.800895694974772 -6.802513429734919 +6.802513429734911 +6.800895694974741 current time step is 700 current time step is 720 current time step is 740 -6.800686842176662 +6.800686842176637 current time step is 760 -6.801545423101174 +6.801545423101133 current time step is 780 current time step is 800 -6.800557966697346 -6.801625648105528 +6.800557966697301 +6.801625648105461 current time step is 820 -6.800409953971007 +6.800409953971042 current time step is 840 current time step is 860 current time step is 880 -6.802851576849863 +6.802851576849832 current time step is 900 current time step is 920 -6.800308721184406 -6.803093891584433 +6.800308721184362 +6.803093891584564 current time step is 940 -6.800466916213642 -6.804489156110476 +6.80046691621362 +6.804489156110395 current time step is 960 current time step is 980 -Run time is 488.412 seconds +Run time is 1122.674 seconds diff --git a/spatial_decompose/job.sh b/spatial_decompose/job.sh index 816ac6f..9b594c5 100644 --- a/spatial_decompose/job.sh +++ b/spatial_decompose/job.sh @@ -1,6 +1,6 @@ #!/bin/bash #SBATCH -N 1 -#SBATCH -n 16 +#SBATCH -n 1 #SBATCH -p RM-small #SBATCH --mem-per-cpu=2000M #SBATCH -e job.err @@ -10,4 +10,5 @@ conda activate dpgpu # module load openmpi/4.0.5-gcc10.2.0 echo $(which mpirun) -~/.conda/envs/dpgpu/bin/mpirun -np $SLURM_NTASKS python MDargon_spatial.py \ No newline at end of file +# ~/.conda/envs/dpgpu/bin/mpirun -np $SLURM_NTASKS python MDargon_spatial.py +~/.conda/envs/dpgpu/bin/mpirun -np $SLURM_NTASKS python MDargon_serial.py \ No newline at end of file diff --git a/spatial_decompose/results_before_PE_parallel/MDargon.py b/spatial_decompose/results_before_PE_parallel/MDargon.py new file mode 100644 index 0000000..2093e2d --- /dev/null +++ b/spatial_decompose/results_before_PE_parallel/MDargon.py @@ -0,0 +1,122 @@ +import numpy as np +import time +import copy +from LJ_SpatialDecomp import * +import utils_spatial_decompose as ut +from mpi4py import MPI + +# MPI initialize +comm = MPI.COMM_WORLD +rank = comm.Get_rank() +size = comm.Get_size() +print(rank,size) +comm.barrier() + +# run params +stop_step=1000 +k_B=1.38064852*10**(-23) +dt=0.002 +file_name='../data/initial_position_LJ_argon256.txt' +info_init=np.loadtxt(file_name) +num_atoms=info_init.shape[0] + +a_init=np.zeros((num_atoms,3)) +r_c=1.6 +L0=6.8 +#cube division +subdiv=np.array([int(np.sqrt(size)),int(np.sqrt(size)),1]) +energy_scale=1.66*10**(-21)#unit: J, Argon +sigma=3.4 #unit: Ang, Argon +T_dimensional_equal=300#unit K +T_equal=T_dimensional_equal*k_B/energy_scale +part_type='LJ' +name='argon256' + + + +if rank==0: + start_time = time.time() + # # initialize + k_B=1.38064852*10**(-23) + size_sim=info_init.shape[0] + # x_dot_init=ut.random_vel_generator(size_sim,T_equal,energy_scale) + #initialize PE, KE, T_insta, P_insta, Momentum + PE=np.zeros((stop_step+1,1)) + KE=np.zeros((stop_step+1,1)) + T_insta=np.zeros((stop_step+1,1)) + P_insta=np.zeros((stop_step+1,1)) + #initialize the info matrix + info=np.zeros((stop_step+1,size_sim,9)) + # info[0,:,:]=np.concatenate((position_init,x_dot_init,a_init),axis=1) + info[0,:,:] = info_init + # np.savetxt('../data/init.txt',info[0,:,:],fmt='%.6f') + infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L0) + #zero step value + PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_c,L=L0) + KE[0,:]=ut.Kin_Eng(info[0,:,3:6]) + T_insta[0,:]=2*KE[0,:]*energy_scale/(3*(size_sim-1)*k_B) #k + P_insta[0,:]=ut.insta_pressure(L0,T_insta[0],info[0,:,0:3],r_c,energy_scale) #unitless +else: + infotodic = None + # info = None +comm.barrier() +infotodic = comm.bcast(infotodic, root = 0) + +# Run MD +for step in range(stop_step): + my_spd_send=utp.vel_Ver( + comm = comm, + infodict=infotodic, + dt=dt, + r_limit=r_c, + L=L0, + my_rank=rank + ) + temp_infodict=comm.gather(my_spd_send,root=0) + if rank == 0: + if step%20==0: + print('current time step is ', step) + temp_infodict=list(filter(None, temp_infodict)) + info_temp=dict(temp_infodict) + tmp=ut.concatDict(info_temp) + info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) + # info[step+1,:,:] = np.round(info[step+1,:,:],4) + info[step+1,:,0:3] = ut.pbc1(info[step+1,:,0:3],L=L0) + #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES + infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) + #calculate and store PE, KE, T_insta, P_insta + PE[step+1,:]=ut.LJ_potent_nondimen(info[step+1,:,0:3],r_cut=r_c,L=L0) + KE[step+1,:]=ut.Kin_Eng(info[step+1,:,3:6]) + T_insta[step+1,:]=2*KE[step+1,:]*energy_scale/(3*(size_sim-1)*k_B) #k + P_insta[step+1,:]=ut.insta_pressure(L0,T_insta[step+1],info[step+1,:,0:3],r_c,energy_scale) #unitless + comm.barrier() + infotodic=comm.bcast(infotodic,root=0) + +if rank == 0: + end_time = time.time() + period = end_time-start_time + print(f'Run time is {period:.3f} seconds') + PE = np.round(PE,4) + KE = np.round(KE,4) + T_insta = np.round(T_insta,4) + P_insta = np.round(P_insta,4) + ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, size, False) +comm.barrier() + +# if rank==0: +# start_time=time.time() +# info,PE,KE,T_insta,P_insta=LJ_MD(subdiv=subdiv, +# position_init=position_init, +# dt=dt, +# stop_step=stop_step, +# accel_init=a_init, +# r_cut=2.8, +# L=L0, +# T_eq=T_equal, +# e_scale=energy_scale, +# sig=sigma) +# end_time=time.time() +# period = end_time-start_time +# print("For this {} steps operation (dt={}) with r_cut = {} and L = {}, it took:".format(stop_step,dt,r_c,L0),end_time-start_time,'s') +# ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, 1000, False) +# else: \ No newline at end of file diff --git a/spatial_decompose/results/argon256_Energy_Temp_Pres.csv b/spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres.csv similarity index 100% rename from spatial_decompose/results/argon256_Energy_Temp_Pres.csv rename to spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres.csv diff --git a/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv b/spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres16core.csv similarity index 100% rename from spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv rename to spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres16core.csv diff --git a/spatial_decompose/results/argon256_Energy_Temp_Pres4core.csv b/spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres1core.csv similarity index 100% rename from spatial_decompose/results/argon256_Energy_Temp_Pres4core.csv rename to spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres1core.csv diff --git a/spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres4core.csv b/spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres4core.csv new file mode 100644 index 0000000..49ad0d8 --- /dev/null +++ b/spatial_decompose/results_before_PE_parallel/argon256_Energy_Temp_Pres4core.csv @@ -0,0 +1,1002 @@ +step,KE,PE,T_insta,P_insta +0,391.3016,-413.596,123.0,4.6302 +1,391.1757,-413.0689,122.9604,4.6414 +2,390.2474,-411.739,122.6686,4.664 +3,388.517,-409.6077,122.1247,4.6978 +4,385.9866,-406.6782,121.3293,4.7423 +5,382.6609,-402.9571,120.2839,4.7976 +6,378.5487,-398.4554,118.9913,4.8636 +7,373.6629,-393.188,117.4555,4.9398 +8,368.021,-387.1753,115.6821,5.026 +9,361.6462,-380.4436,113.6783,5.1217 +10,354.5682,-373.0263,111.4534,5.2262 +11,346.8243,-364.9646,109.0192,5.3389 +12,338.46,-356.3091,106.39,5.4588 +13,329.5307,-347.1198,103.5832,5.585 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spatial_decompose/results/argon256_summary.txt rename to spatial_decompose/results_before_PE_parallel/argon256_summary.txt diff --git a/spatial_decompose/results/argon256core16_summary.txt b/spatial_decompose/results_before_PE_parallel/argon256core16_summary.txt similarity index 100% rename from spatial_decompose/results/argon256core16_summary.txt rename to spatial_decompose/results_before_PE_parallel/argon256core16_summary.txt diff --git a/spatial_decompose/results/argon256iter1.txt b/spatial_decompose/results_before_PE_parallel/argon256iter1.txt similarity index 100% rename from spatial_decompose/results/argon256iter1.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter1.txt diff --git a/spatial_decompose/results/argon256iter1000.txt b/spatial_decompose/results_before_PE_parallel/argon256iter1000.txt similarity index 100% rename from spatial_decompose/results/argon256iter1000.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter1000.txt diff --git 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spatial_decompose/results/argon256iter1000core16_summary.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter1000core16_summary.txt diff --git a/spatial_decompose/results_before_PE_parallel/argon256iter1000core1_summary.txt b/spatial_decompose/results_before_PE_parallel/argon256iter1000core1_summary.txt new file mode 100644 index 0000000..6364c2d --- /dev/null +++ b/spatial_decompose/results_before_PE_parallel/argon256iter1000core1_summary.txt @@ -0,0 +1,6 @@ +Simulation Cell Size(unitless): 6.8 +Simulation Particles Amount: 256 +File Name: argon256 +Simulation Time: 1122.673855304718 +Simulation Step: 1000 +Force Cut-off: 1.6 diff --git a/spatial_decompose/results/argon256iter1000core4.txt b/spatial_decompose/results_before_PE_parallel/argon256iter1000core4.txt similarity index 100% rename from spatial_decompose/results/argon256iter1000core4.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter1000core4.txt diff --git a/spatial_decompose/results/argon256iter1000core4_summary.txt b/spatial_decompose/results_before_PE_parallel/argon256iter1000core4_summary.txt similarity index 100% rename from spatial_decompose/results/argon256iter1000core4_summary.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter1000core4_summary.txt diff --git a/spatial_decompose/results/argon256iter10core16.txt b/spatial_decompose/results_before_PE_parallel/argon256iter10core16.txt similarity index 100% rename from spatial_decompose/results/argon256iter10core16.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter10core16.txt diff --git a/spatial_decompose/results/argon256iter10core4.txt b/spatial_decompose/results_before_PE_parallel/argon256iter10core4.txt similarity index 100% rename from spatial_decompose/results/argon256iter10core4.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter10core4.txt diff --git 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0.264656 -0.359256 6.116302 -0.178882 6.116302 +5.413985 5.414566 4.640620 -0.360698 -0.069897 -0.278122 6.116302 6.116302 -0.178882 diff --git a/spatial_decompose/results_before_PE_parallel/argon256iter1core1_summary.txt b/spatial_decompose/results_before_PE_parallel/argon256iter1core1_summary.txt new file mode 100644 index 0000000..f73c9ea --- /dev/null +++ b/spatial_decompose/results_before_PE_parallel/argon256iter1core1_summary.txt @@ -0,0 +1,6 @@ +Simulation Cell Size(unitless): 6.8 +Simulation Particles Amount: 256 +File Name: argon256 +Simulation Time: 1.677480697631836 +Simulation Step: 1 +Force Cut-off: 1.6 diff --git a/spatial_decompose/results/argon256iter1core4.txt b/spatial_decompose/results_before_PE_parallel/argon256iter1core4.txt similarity index 100% rename from spatial_decompose/results/argon256iter1core4.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter1core4.txt diff --git a/spatial_decompose/results/argon256iter2core16.txt b/spatial_decompose/results_before_PE_parallel/argon256iter2core16.txt similarity index 100% rename from spatial_decompose/results/argon256iter2core16.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter2core16.txt diff --git a/spatial_decompose/results/argon256iter2core4.txt b/spatial_decompose/results_before_PE_parallel/argon256iter2core4.txt similarity index 100% rename from spatial_decompose/results/argon256iter2core4.txt rename to spatial_decompose/results_before_PE_parallel/argon256iter2core4.txt diff --git a/spatial_decompose/utils_spatial_decompose.py b/spatial_decompose/utils_spatial_decompose.py index a9b5085..ee6d7f3 100644 --- a/spatial_decompose/utils_spatial_decompose.py +++ b/spatial_decompose/utils_spatial_decompose.py @@ -308,7 +308,7 @@ def LJ_accel(position,neighb_x_0,r_cut,L, rank): accel=np.zeros((r_relat.shape[0],3)) flag = 0 for i, r0 in enumerate(r_relat): - if r0 <= r_cut: + if r0 <= r_cut and r0!=0: separation_active_num=separation_new[i,:] vector_part=separation_active_num*(1/r0) scalar_part=48*r0**(-13)-24*r0**(-7)-dU_drcut From 4cea7b156be80bea8e2ad30cf1a3df5ef68107b8 Mon Sep 17 00:00:00 2001 From: Hancheng Zhao Date: Fri, 5 Jan 2024 02:31:11 -0500 Subject: [PATCH 7/9] improved efficiency of parallel program, seems to have super linear scaling now --- spatial_decompose/MDargon_serial.py | 54 +- spatial_decompose/MDargon_spatial.py | 72 +- .../__pycache__/utils.cpython-39.pyc | Bin 0 -> 8890 bytes .../__pycache__/utils_parallel.cpython-39.pyc | Bin 974 -> 974 bytes .../utils_spatial_decompose.cpython-310.pyc | Bin 8575 -> 8711 bytes .../utils_spatial_decompose.cpython-39.pyc | Bin 8567 -> 8721 bytes spatial_decompose/job.out | 86 -- spatial_decompose/job.sh | 2 +- .../argon256_Energy_Temp_Pres16core.csv | 1002 +++++++++++++++++ .../argon256_Energy_Temp_Pres1core.csv | 3 + .../argon256_Energy_Temp_Pres4core.csv | 1002 +++++++++++++++++ .../results/argon256iter1000core1.txt | 256 +++++ .../results/argon256iter1000core16.txt | 256 +++++ .../argon256iter1000core16_summary.txt | 6 + .../results/argon256iter1000core1_summary.txt | 6 + .../results/argon256iter1000core4.txt | 256 +++++ .../results/argon256iter1000core4_summary.txt | 6 + .../results/argon256iter1core1.txt | 256 +++++ .../results/argon256iter1core16.txt | 256 +++++ .../results/argon256iter1core16_summary.txt | 6 + .../results/argon256iter1core1_summary.txt | 6 + .../results/argon256iter1core4.txt | 256 +++++ .../results/argon256iter1core4_summary.txt | 6 + .../results/argon256iter2core1.txt | 256 +++++ .../results/argon256iter2core1_summary.txt | 6 + .../results/argon256position_last1stps.xyz | 258 +++++ spatial_decompose/utils.py | 338 ++++++ spatial_decompose/utils_spatial_decompose.py | 39 +- 28 files changed, 4534 insertions(+), 156 deletions(-) create mode 100644 spatial_decompose/__pycache__/utils.cpython-39.pyc create mode 100644 spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv create mode 100644 spatial_decompose/results/argon256_Energy_Temp_Pres1core.csv create mode 100644 spatial_decompose/results/argon256_Energy_Temp_Pres4core.csv create mode 100644 spatial_decompose/results/argon256iter1000core1.txt create mode 100644 spatial_decompose/results/argon256iter1000core16.txt create mode 100644 spatial_decompose/results/argon256iter1000core16_summary.txt create mode 100644 spatial_decompose/results/argon256iter1000core1_summary.txt create mode 100644 spatial_decompose/results/argon256iter1000core4.txt create mode 100644 spatial_decompose/results/argon256iter1000core4_summary.txt create mode 100644 spatial_decompose/results/argon256iter1core1.txt create mode 100644 spatial_decompose/results/argon256iter1core16.txt create mode 100644 spatial_decompose/results/argon256iter1core16_summary.txt create mode 100644 spatial_decompose/results/argon256iter1core1_summary.txt create mode 100644 spatial_decompose/results/argon256iter1core4.txt create mode 100644 spatial_decompose/results/argon256iter1core4_summary.txt create mode 100644 spatial_decompose/results/argon256iter2core1.txt create mode 100644 spatial_decompose/results/argon256iter2core1_summary.txt create mode 100644 spatial_decompose/results/argon256position_last1stps.xyz create mode 100644 spatial_decompose/utils.py diff --git a/spatial_decompose/MDargon_serial.py b/spatial_decompose/MDargon_serial.py index 7597818..cfcd702 100644 --- a/spatial_decompose/MDargon_serial.py +++ b/spatial_decompose/MDargon_serial.py @@ -2,7 +2,9 @@ import time import copy from LJ_SpatialDecomp import * -import utils_spatial_decompose as ut +# import utils_spatial_decompose as ut +import utils as ut +import utils_spatial_decompose from mpi4py import MPI @@ -38,12 +40,14 @@ def LJ_acc(position,r_cut,L, rank): # print(accel[accel.any(axis=1)],r_relat[a return update_accel.reshape(subcube_atoms,3) -# MPI initialize -comm = MPI.COMM_WORLD -rank = comm.Get_rank() -size = comm.Get_size() -print(rank,size) -comm.barrier() +# # MPI initialize +# comm = MPI.COMM_WORLD +# rank = comm.Get_rank() +# size = comm.Get_size() +# print(rank,size) +# comm.barrier() +rank = 0 +size = 1 # run params stop_step=1000 @@ -65,42 +69,42 @@ def LJ_acc(position,r_cut,L, rank): part_type='LJ' name='argon256' +#initialize PE, KE, T_insta, P_insta, Momentum +PE=np.zeros((stop_step+1,1)) +KE=np.zeros((stop_step+1,1)) +T_insta=np.zeros((stop_step+1,1)) +P_insta=np.zeros((stop_step+1,1)) + # if rank==0: -start_time = time.time() + # # initialize k_B=1.38064852*10**(-23) size_sim=info_init.shape[0] # x_dot_init=ut.random_vel_generator(size_sim,T_equal,energy_scale) -#initialize PE, KE, T_insta, P_insta, Momentum -PE=np.zeros((stop_step+1,1)) -KE=np.zeros((stop_step+1,1)) -T_insta=np.zeros((stop_step+1,1)) -P_insta=np.zeros((stop_step+1,1)) #initialize the info matrix info=np.zeros((stop_step+1,size_sim,9)) # info[0,:,:]=np.concatenate((position_init,x_dot_init,a_init),axis=1) +start_time = time.time() info[0,:,:] = info_init # np.savetxt('../data/init.txt',info[0,:,:],fmt='%.6f') -infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L0) +# infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L0) +my_spd = ut.SpatialDomainData(info[0,:,0:3],info[0,:,3:6],info[0,:,6:9]) #zero step value -PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_c,L=L0) +PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_c,L=L0)/2 KE[0,:]=ut.Kin_Eng(info[0,:,3:6]) T_insta[0,:]=2*KE[0,:]*energy_scale/(3*(size_sim-1)*k_B) #k -P_insta[0,:]=ut.insta_pressure(L0,T_insta[0],info[0,:,0:3],r_c,energy_scale) #unitless +P_insta[0,:]=ut.insta_pressure(L0,T_insta[0],info[0,:,0:3],r_c,energy_scale)/2 #unitless # Run MD for step in range(stop_step): - # neighboring atoms - neighb_spd = infotodic[0] - my_spd = infotodic[0] - my_spd.A = ut.LJ_accel(position=my_spd.P,neighb_x_0=neighb_spd.P,r_cut=r_c,L=L0,rank=0)/2.0 + my_spd.A = LJ_acc(position=my_spd.P,r_cut=r_c,L=L0,rank=0) my_spd.V=my_spd.V+my_spd.A*(dt) my_spd.P=my_spd.P+my_spd.V*dt my_spd.P=ut.pbc1(position=my_spd.P,L=L0) if step%20==0: print('current time step is ', step) - temp_infodict = (0,my_spd) - temp_infodict=list(filter(None, temp_infodict)) + # temp_infodict = (0,my_spd) + # temp_infodict=list(filter(None, temp_infodict)) temp_infodict = [(0,my_spd)] info_temp=dict(temp_infodict) # print(info_temp) @@ -109,8 +113,8 @@ def LJ_acc(position,r_cut,L, rank): # info[step+1,:,:] = np.round(info[step+1,:,:],4) info[step+1,:,0:3] = ut.pbc1(info[step+1,:,0:3],L=L0) #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES - infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) - + # infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) + #calculate and store PE, KE, T_insta, P_insta in parallel PE[step+1,:]=ut.LJ_potent_nondimen(info[step+1,:,0:3],r_cut=r_c,L=L0) KE[step+1,:]=ut.Kin_Eng(info[step+1,:,3:6]) @@ -125,7 +129,7 @@ def LJ_acc(position,r_cut,L, rank): KE = np.round(KE,4) T_insta = np.round(T_insta,4) P_insta = np.round(P_insta,4) -ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, size, False) +utils_spatial_decompose.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, size, False) # if rank==0: # start_time=time.time() diff --git a/spatial_decompose/MDargon_spatial.py b/spatial_decompose/MDargon_spatial.py index 94cddcd..62fadae 100644 --- a/spatial_decompose/MDargon_spatial.py +++ b/spatial_decompose/MDargon_spatial.py @@ -32,35 +32,43 @@ part_type='LJ' name='argon256' - +#initialize PE, KE, T_insta, P_insta, Momentum +PE=np.zeros((stop_step+1,1)) +KE=np.zeros((stop_step+1,1)) +T_insta=np.zeros((stop_step+1,1)) +P_insta=np.zeros((stop_step+1,1)) if rank==0: start_time = time.time() # # initialize k_B=1.38064852*10**(-23) size_sim=info_init.shape[0] - # x_dot_init=ut.random_vel_generator(size_sim,T_equal,energy_scale) - #initialize PE, KE, T_insta, P_insta, Momentum - PE=np.zeros((stop_step+1,1)) - KE=np.zeros((stop_step+1,1)) - T_insta=np.zeros((stop_step+1,1)) - P_insta=np.zeros((stop_step+1,1)) + # x_dot_init=ut.random_vel_generator(size_sim,T_equal,energy_scale) #initialize the info matrix info=np.zeros((stop_step+1,size_sim,9)) # info[0,:,:]=np.concatenate((position_init,x_dot_init,a_init),axis=1) info[0,:,:] = info_init # np.savetxt('../data/init.txt',info[0,:,:],fmt='%.6f') infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L0) - #zero step value - PE[0,:]=ut.LJ_potent_nondimen(info[0,:,0:3],r_cut=r_c,L=L0) - KE[0,:]=ut.Kin_Eng(info[0,:,3:6]) + KE[0,:] = ut.Kin_Eng(info[0,:,3:6]) T_insta[0,:]=2*KE[0,:]*energy_scale/(3*(size_sim-1)*k_B) #k - P_insta[0,:]=ut.insta_pressure(L0,T_insta[0],info[0,:,0:3],r_c,energy_scale) #unitless + print(T_insta[0,:][0]) else: infotodic = None - # info = None -# comm.barrier() +comm.barrier() infotodic = comm.bcast(infotodic, root = 0) +T_single = comm.bcast(T_insta[0,:][0], root=0) + +my_spd, neighs_spd = ut.separate_points(infotodic, my_rank = rank, nproc = size) +#zero step value +PE_single=ut.LJ_potent_nondimen(my_spd.P,neighs_spd.P,r_cut=r_c,L=L0) +P_single=ut.insta_pressure(L0,T_single,my_spd.P,neighs_spd.P,r_c,energy_scale) #unitless +PE_all = comm.reduce(PE_single,op=MPI.SUM,root=0) +P_all = comm.reduce(P_single,op=MPI.SUM,root=0) + +if rank==0: + PE[0,:] = PE_all + P_insta[0,:] = P_all # Run MD for step in range(stop_step): @@ -73,18 +81,15 @@ my_rank=rank ) # apply periodic boundary condition - my_spd_send[1].P = ut.pbc1(my_spd_send[1].P,L=L0) - #calculate and store PE, KE, T_insta, P_insta in parallel - PE_single = ut.LJ_potent_nondimen(my_spd_send[1].P,r_cut=r_c,L=L0) + my_spd_send[1].P = ut.pbc1(my_spd_send[1].P,L=L0) + #calculate and store KE in parallel KE_single = ut.Kin_Eng(my_spd_send[1].V) - T_single = 2*KE_single*energy_scale/(3*(my_spd_send[1].P.shape[0]-1)*k_B) #k - # P_single = ut.insta_pressure(L0,) # gather temp_infodict=comm.gather(my_spd_send,root=0) - comm.reduce([PE_single,MPI.FLOAT],None,op=MPI.SUM,root=0) - comm.reduce([KE_single,MPI.FLOAT],None,op=MPI.SUM,root=0) - comm.reduce([T_single,MPI.FLOAT],None,op=MPI.SUM,root=0) + KE_all = comm.reduce(KE_single,op=MPI.SUM,root=0) + # T_all = comm.reduce(T_single,op=MPI.SUM,root=0) + # P_all = comm.reduce(P_single, op=MPI.SUM, root=0) if rank == 0: if step%20==0: @@ -97,14 +102,25 @@ # info[step+1,:,0:3] = ut.pbc1(info[step+1,:,0:3],L=L0) #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) - - #calculate and store PE, KE, T_insta, P_insta in parallel - PE[step+1,:]=PE_single - KE[step+1,:]=KE_single - T_insta[step+1,:]=T_single/size - # P_insta[step+1,:]=ut.insta_pressure(L0,T_insta[step+1],info[step+1,:,0:3],r_c,energy_scale) #unitless + # gather KE and T + KE[step+1,:]=KE_all + T_insta[step+1,:]=2*KE_all*energy_scale/(3*(size_sim-1)*k_B) #k + comm.barrier() + infotodic = comm.bcast(infotodic, root = 0) + T_single = comm.bcast(T_insta[step+1,:][0], root = 0) + # calculate PE,P in parallel + my_spd, neighs_spd = ut.separate_points(infotodic, my_rank = rank, nproc = size) + PE_single = ut.LJ_potent_nondimen(position = my_spd.P, position_neighbor = neighs_spd.P, r_cut = r_c, L=L0) + P_single = ut.insta_pressure(L0,T_single,my_spd.P,neighs_spd.P,r_c,energy_scale) + # gather back to 0 + PE_all = comm.reduce(PE_single,op=MPI.SUM,root=0) + P_all = comm.reduce(P_single,op=MPI.SUM,root=0) + if rank==0: + #calculate and store PE, P_insta + PE[step+1,:]=PE_all + P_insta[step+1,:]=P_all # comm.barrier() - infotodic=comm.bcast(infotodic,root=0) + # infotodic=comm.bcast(infotodic,root=0) if rank == 0: end_time = time.time() diff --git a/spatial_decompose/__pycache__/utils.cpython-39.pyc b/spatial_decompose/__pycache__/utils.cpython-39.pyc new file mode 100644 index 0000000000000000000000000000000000000000..f566516c447077951585ff0c3441240b95ae74f5 GIT 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7b5f150..980a382 100644 --- a/spatial_decompose/job.out +++ b/spatial_decompose/job.out @@ -1,87 +1 @@ /opt/intel/oneapi/intelpython/latest/bin/mpirun -0 1 -current time step is 0 -current time step is 20 -current time step is 40 -current time step is 60 -current time step is 80 -6.800088657224866 -current time step is 100 -current time step is 120 -current time step is 140 -current time step is 160 -current time step is 180 -current time step is 200 -current time step is 220 -6.800887957082665 -6.800481721319658 -6.801291421279881 -current time step is 240 -current time step is 260 -current time step is 280 -current time step is 300 -6.801071355170859 -current time step is 320 -current time step is 340 -current time step is 360 -current time step is 380 -6.800504763517788 -current time step is 400 -current time step is 420 -current time step is 440 -6.802346649248438 -6.801138516114347 -6.802031021387377 -current time step is 460 -6.800763838812505 -current time step is 480 -6.800891791633579 -6.802358924955001 -current time step is 500 -6.800859721949975 -current time step is 520 -6.801626610851167 -6.802377691457667 -current time step is 540 -current time step is 560 -6.801050444814723 -6.803229807623386 -current time step is 580 -6.8004510420618836 -6.801097917985061 -current time step is 600 -6.800872792845088 -current time step is 620 -current time step is 640 -6.802398062547355 -6.800161513604764 -current time step is 660 -current time step is 680 -6.802513429734911 -6.800895694974741 -current time step is 700 -current time step is 720 -current time step is 740 -6.800686842176637 -current time step is 760 -6.801545423101133 -current time step is 780 -current time step is 800 -6.800557966697301 -6.801625648105461 -current time step is 820 -6.800409953971042 -current time step is 840 -current time step is 860 -current time step is 880 -6.802851576849832 -current time step is 900 -current time step is 920 -6.800308721184362 -6.803093891584564 -current time step is 940 -6.80046691621362 -6.804489156110395 -current time step is 960 -current time step is 980 -Run time is 1122.674 seconds diff --git a/spatial_decompose/job.sh b/spatial_decompose/job.sh index 9b594c5..99212b5 100644 --- a/spatial_decompose/job.sh +++ b/spatial_decompose/job.sh @@ -11,4 +11,4 @@ conda activate dpgpu # module load openmpi/4.0.5-gcc10.2.0 echo $(which mpirun) # ~/.conda/envs/dpgpu/bin/mpirun -np $SLURM_NTASKS python MDargon_spatial.py -~/.conda/envs/dpgpu/bin/mpirun -np $SLURM_NTASKS python MDargon_serial.py \ No newline at end of file +python MDargon_serial.py \ No newline at end of file diff --git a/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv b/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv new file mode 100644 index 0000000..49ad0d8 --- /dev/null +++ b/spatial_decompose/results/argon256_Energy_Temp_Pres16core.csv @@ -0,0 +1,1002 @@ +step,KE,PE,T_insta,P_insta +0,391.3016,-413.596,123.0,4.6302 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4.64155422 3.08871361 1.5491846 +LJ 4.64326777 3.86016332 2.3196390 +LJ 5.41579573 3.09499841 2.3188506 +LJ 5.41813864 3.87191733 1.5439347 +LJ 4.64181415 3.09129729 3.0868189 +LJ 4.63836289 3.87159035 3.8717238 +LJ 5.41356967 3.09770742 3.8644223 +LJ 5.42289867 3.87141457 3.0940537 +LJ 4.64524732 3.09492811 4.6472269 +LJ 4.64677646 3.86813134 5.4220461 +LJ 5.40621359 3.09593135 5.4213442 +LJ 5.41747608 3.86760973 4.6391023 +LJ 4.63685834 4.64140176 6.7995932 +LJ 4.63362969 5.41969627 0.7678424 +LJ 5.41854893 4.64767823 0.7784051 +LJ 5.41376288e+00 5.41841132e+00 3.18544164e-0 +LJ 4.64608865 4.64496737 1.5450503 +LJ 4.63751001 5.41741332 2.3241625 +LJ 5.41703856 4.63454681 2.3259166 +LJ 5.41720527 5.4123228 1.5526452 +LJ 4.63232657 4.63347795 3.0884249 +LJ 4.64332578 5.40854564 3.8673383 +LJ 5.42156812 4.64835398 3.8696404 +LJ 5.41159285 5.41320785 3.0937280 +LJ 4.64632379 4.63774988 4.6407581 +LJ 4.63932884 5.4097154 5.4089161 +LJ 5.41660145 4.64223375 5.4132937 +LJ 5.41328882 5.41445243 4.6400637 diff --git a/spatial_decompose/utils.py b/spatial_decompose/utils.py new file mode 100644 index 0000000..557d0bb --- /dev/null +++ b/spatial_decompose/utils.py @@ -0,0 +1,338 @@ +import numpy as np +import numba +from numba.experimental import jitclass +from numba import float64 +from numba.typed import Dict +from numba.core import types +import os +import pandas as pd +import copy +#first the dtypes of the input matrices need to be explicitly clarified +class SpatialDomainData: + #This class creates objects for storing position, velocity and acceleration information + ##This class contain three functions: + ###__init__ (description) + ###__repr__ (description) + ###concat(description) + def __init__(self, position=np.array([]), velocity=np.array([]), acceleration=np.array([])): + self.P = position + self.V = velocity + self.A = acceleration + + def __repr__(self): + return "(P:{}, V:{}, A:{})".format(self.P, self.V, self.A) + + def concat(self, other): + self.P = np.concatenate((self.P, other.P), 0) + self.V = np.concatenate((self.V, other.V), 0) + self.A = np.concatenate((self.A, other.A), 0) + +@numba.njit +def pbc1(position,L): + ##This function perform the first rule of periodic boundary condition + #Input: position -- the position before PBC1 + # L -- the simulation cell size + #Ouput: x_new -- the updated position after PBC1 + position_new=np.zeros((position.shape[0],3)) + for i in range(position.shape[0]): + position_ind=position[i,:] + position_empty=np.zeros((1,3)) + for j in range(3): + position_axis=numba.float64(position_ind[j]) + if position_axis < 0: + position_axis_new=position_axis+L + elif position_axis > L: + position_axis_new=position_axis-L + else: + position_axis_new=position_axis + position_empty[:,j]=position_axis_new + position_new[i,:]=position_empty + return position_new + +@numba.njit +def pbc2(separation,L): + ##This function perform the second rule of periodic boundary condition + #Input: separation -- separation before PBC2 + # L -- the simulation cell size + #Ouput: separation_new -- the updated separation after PBC2 + separation_new=np.zeros((separation.shape[0],3)) + for i in range(separation.shape[0]): + separation_ind=separation[i,:] + separation_empty=np.zeros((1,3)) + for j in range(3): + separation_axis=numba.float64(separation_ind[j]) + if separation_axis < -L/2: + separation_axis_new=separation_axis+L + elif separation_axis > L/2: + separation_axis_new=separation_axis-L + else: + separation_axis_new=separation_axis + separation_empty[:,j]=separation_axis_new + separation_new[i,:]=separation_empty + return separation_new + +@numba.njit +def random_vel_generator(n,T_equal,e_scale): + ##This function generate random initial velocity at the desired temperature + #Input: n -- number of atoms + # T_equal -- the temperature of interests + # e_scale -- the energy scale of the particle of interests + #Ouput: vel_per_particle -- the velocity matrix assigned to all particles + total_k=3*T_equal*(n-1)/2 + vel_per_particle=np.zeros((n,3)) + for axis in range(3): + vel_per_particle[:,axis]=np.random.randn(n,)-0.5 + Mom_x_total=np.sum(vel_per_particle[:,0]) + Mom_y_total=np.sum(vel_per_particle[:,1]) + Mom_z_total=np.sum(vel_per_particle[:,2]) + Mom_x_avg=Mom_x_total/n + Mom_y_avg=Mom_y_total/n + Mom_z_avg=Mom_z_total/n + vel_per_particle=vel_per_particle-np.array([Mom_x_avg,Mom_y_avg,Mom_z_avg]).reshape(1,3) + k_avg_init=0.5*(1/n)*np.sum(np.sum(vel_per_particle**2,axis=1),axis=0) + k_avg_T_eq=total_k/n + scaling_ratio=np.sqrt(k_avg_T_eq/k_avg_init) + vel_per_particle=vel_per_particle*scaling_ratio + return vel_per_particle + +@numba.njit +def Kin_Eng(velocity): + ##This function compute the average kinetic energy of the system at given the velocity + #Input: velocity -- the velocities of all the particles + #Output: Kinetic_sum -- the average kinetic energy of the system + num=velocity.shape[0] + Kinetic_per=0.5*np.sum(velocity**2,axis=1) + Kinetic_avg=np.sum(Kinetic_per,axis=0) + return Kinetic_avg + +@numba.njit +def LJ_potent_nondimen(position,r_cut,L): + ##This function compute the nondimensional potential energy of the system at the given position + #Input: position -- the position of all the particles at this instance + # r_cut -- the cutoff for the short-range force field + # L -- the size of the simulation cell + #Output: np.sum(update_LJ) -- the potential energy of the system at this instance + num=position.shape[0] + update_LJ=np.zeros((num-1,1)) + #fix value for a certain r_limit + dU_drcut=24*r_cut**(-7)-48*r_cut**(-13) + U_rcut=4*(r_cut**(-12)-r_cut**(-6)) + for atom in range(num-1): + position_relevent=position[atom:,:] + position_other=position_relevent[1:,:] + #pbc rule2 + separation=position_relevent[0,:]-position_other + separation_new=pbc2(separation=separation,L=L) + r_relat=np.sqrt(np.sum(separation_new**2,axis=1)).reshape(separation_new.shape[0],) + LJ=[] + #get out the particles inside the r_limit + for r0 in r_relat: + if r0 <= r_cut: + LJ_num=4*r0**(-12)-4*r0**(-6)-U_rcut-(r0-r_cut)*dU_drcut + LJ.append(LJ_num) + update_LJ[atom,:]=np.sum(np.array(LJ),axis=0) + return np.sum(update_LJ) + +@numba.njit +def insta_pressure(L,T,position,r_cut,e_scale): + ##This function computes the dimensionless pressure + #Inputs: L -- The size of the simulation cell + # T -- The simulation temperature + # position -- The position of all the particles at this time step + # e_scale -- The energy scale of this particles + #Ouputs: pres_insta -- The instant pressure at this moment + num=position.shape[0] + k_B=1.38064852*10**(-23) + V=L**3 + pres_ideal=num*T*(k_B/e_scale)/V + dU_drcut=24*r_cut**(-7)-48*r_cut**(-13) + pres_virial=np.zeros((num-1,1)) + for atom in range(num-1): + position_relevent=position[atom:,:] + position_other=position_relevent[1:,:] + position_atom=position_relevent[0,:] + #pbc rule 2 + separation=position_atom-position_other + separation_new=pbc2(separation=separation,L=L) + r_relat=np.sqrt(np.sum(separation_new**2,axis=1)).reshape(separation_new.shape[0],) + force=[] + active_r_relat=[] + #get out the particles inside the r_limit + for r0 in r_relat: + if r0 <= r_cut: + #active_r_relat.append(r0) + force_num=-(24*r0**(-7)-48*r0**(-13))+dU_drcut + force.append(force_num) + active_r_relat.append(r0) + #get out the particles inside the r_cut + active_amount=np.array(active_r_relat).shape[0] + rijFij=np.array(active_r_relat).reshape(1,active_amount)@np.array(force).reshape(active_amount,1) + pres_virial[atom,:]=rijFij + pres_insta=pres_ideal+np.sum(pres_virial,axis=0)/(3*V) + return pres_insta + +#need to initialize the type before calling the function +float_array = types.float64[:,:] +@numba.njit() +def cell_to_dict(info,nx,ny,nz,L): + ##This is the helper function to create dictionary containing matrix for cell_to_obj + #Inpust: info -- the position + velocity + acceleration of the patricles at the + cell_dict = Dict.empty(key_type=types.int64, value_type=float_array) + xinterval=L/nx + yinterval=L/ny + zinterval=L/nz + #cell_lists={} + for i in range(1,nx*ny*nz+1): + cell_dict[i]= np.zeros((1,9)) + for i in range(info.shape[0]): + atom=info[i,0:9].reshape(1,9) + #check extra one!!! + #if statements !!!!!!! + #check later + atomID=int(((np.floor(atom[:,0]/xinterval)+1+(np.floor(atom[:,1]/yinterval))*ny)+(np.floor(atom[:,2]/zinterval))*(nx*ny))[0]) + cell_dict[atomID]=np.append(cell_dict[atomID],atom,axis=0) + for i in range(1,nx*ny*nz+1): + cell_lists[i]=cell_lists[i][1:,:] + return cell_lists + +def cell_to_obj(positions,nx,ny,nz,L): + cell_lists=cell_to_dict(positions,nx,ny,nz,L) + new_cell_list={} + for i in range(1,nx*ny*nz+1): + # I think this works but we should think more about what an "empty" shape means + # currently when a key points to an empty cube the cube has a position vector of dimensions [0,3] + if cell_lists[i].shape[0]!=0: + temp_reshaped=cell_lists[i] + temp_position = temp_reshaped[:,0:3] + assert(temp_position.shape[1] == 3) + temp_velocity = temp_reshaped[:,3:6] + temp_acceleration = temp_reshaped[:,6:9] + spatial_domain_data = SpatialDomainData(temp_position, + temp_velocity, + temp_acceleration) + new_cell_list[i] = spatial_domain_data + else: + new_cell_list[i] = SpatialDomainData(np.empty((0,3)), + np.empty((0,3)), + np.empty((0,3))) + return new_cell_list + +#@numba.njit() +def separate_points(infodict, my_i): + neighb_spd=None + for i,spd in infodict.items(): + if i!=my_i: + if (neighb_spd is None): + neighb_spd = copy.deepcopy(spd) + else: + neighb_spd.concat(spd) + return infodict[my_i], neighb_spd + +#@numba.njit +def concatDict(infodict): + wholeDict=None + for i,spd in infodict.items(): + if(wholeDict is None): + wholeDict = copy.deepcopy(spd) + else: + wholeDict.concat(spd) + return wholeDict + +#@numba.njit() +def LJ_accel(position,neighb_x_0,r_cut,L): + subcube_atoms=position.shape[0] + #careful kind of confusing + position=np.concatenate((position,neighb_x_0),0) + num=position.shape[0] + update_accel=np.zeros((subcube_atoms,3)) + dU_drcut=48*r_cut**(-13)-24*r_cut**(-7) + #for loop is only of subcube we are interested in but we have to account for ALL distance! + for atom in range(subcube_atoms): + position_other=np.concatenate((position[0:atom,:],position[atom+1:num+1,:]),axis=0) + position_atom=position[atom] + separation=position_atom-position_other + separation_new=pbc2(separation=separation,L=L) + r_relat=np.sqrt(np.sum(separation_new**2,axis=1)) + #get out the particles inside the r_cut + accel=np.zeros((r_relat.shape[0],3)) + for i, r0 in enumerate(r_relat): + if r0 <= r_cut: + separation_active_num=separation_new[i,:] + vector_part=separation_active_num*(1/r0) + scalar_part=48*r0**(-13)-24*r0**(-7)-dU_drcut + accel_num=vector_part*scalar_part + accel[i,:]=accel_num + update_accel[atom,:]=np.sum(accel,axis=0) + return update_accel.reshape(subcube_atoms,3) + +def data_saver(info, PE, KE, T_insta, P_insta, L, num_atoms,part_type,name,period,stop_step, r_c, iterations_int=1000, make_directory=True): + iterations=str(iterations_int) + if make_directory == True: + os.mkdir('results') + path_to_file_xyz="results/"+name+"position_last"+iterations+"stps"+".xyz" + path_to_file_other = "results/"+name+"_Energy_Temp_Pres"+".csv" + path_to_file_summary = "results/"+name+"_summary"+".txt" + p= open(path_to_file_xyz,"w") + s= open(path_to_file_summary,'w') + + #writing xyz file + comment = 'This is the position of the system during the last '+iterations+' steps' + for atoms in info[-int(iterations):,:,0:3]: + p.write("%s\n" % str(num_atoms)) + p.write("%s\n" % comment) + for atom in atoms: + p.write(part_type) + p.write("\t%s\n" % str(atom)[1:-2]) + + #writing other file + other_dict={} + other_dict['KE']=KE.reshape(KE.shape[0],) + other_dict['PE']=PE.reshape(PE.shape[0],) + other_dict['T_insta']=T_insta.reshape(T_insta.shape[0],) + other_dict['P_insta']=P_insta.reshape(P_insta.shape[0],) + other_df=pd.DataFrame.from_dict(other_dict) + other_df.to_csv(path_to_file_other,index_label='step') + + #writing summary file + s.write("Simulation Cell Size(unitless): "+str(L)+"\n") + s.write("Simulation Particles Amount: "+str(num_atoms)+"\n") + s.write("File Name: "+str(name)+"\n") + s.write("Simulation Time: "+ str(period)+"\n") + s.write("Simulation Step: "+str(stop_step)+"\n") + s.write("Force Cut-off: "+str(r_c)+"\n") + p.close() + s.close() + else: + path_to_file_xyz="results/"+name+"position_last"+iterations+"stps"+".xyz" + path_to_file_other = "results/"+name+"_Energy_Temp_Pres"+".csv" + path_to_file_summary = "results/"+name+"_summary"+".txt" + p= open(path_to_file_xyz,"w") + s= open(path_to_file_summary,'w') + + #writing xyz file + comment = 'This is the position of the system during the last '+iterations+' steps' + for atoms in info[-int(iterations):,:,0:3]: + p.write("%s\n" % str(num_atoms)) + p.write("%s\n" % comment) + for atom in atoms: + p.write(part_type) + p.write("\t%s\n" % str(atom)[1:-2]) + + #writing other file + other_dict={} + other_dict['KE']=KE.reshape(KE.shape[0],) + other_dict['PE']=PE.reshape(PE.shape[0],) + other_dict['T_insta']=T_insta.reshape(T_insta.shape[0],) + other_dict['P_insta']=P_insta.reshape(P_insta.shape[0],) + other_df=pd.DataFrame.from_dict(other_dict) + other_df.to_csv(path_to_file_other,index_label='step') + + #writing summary file + s.write("Simulation Cell Size(unitless): "+str(L)+"\n") + s.write("Simulation Particles Amount: "+str(num_atoms)+"\n") + s.write("File Name: "+str(name)+"\n") + s.write("Simulation Time: "+ str(period)+"\n") + s.write("Simulation Step: "+str(stop_step)+"\n") + s.write("Force Cut-off: "+str(r_c)+"\n") + p.close() + s.close() diff --git a/spatial_decompose/utils_spatial_decompose.py b/spatial_decompose/utils_spatial_decompose.py index ee6d7f3..3d7e724 100644 --- a/spatial_decompose/utils_spatial_decompose.py +++ b/spatial_decompose/utils_spatial_decompose.py @@ -109,35 +109,39 @@ def Kin_Eng(velocity): return Kinetic_avg # @numba.njit -def LJ_potent_nondimen(position,r_cut,L): +def LJ_potent_nondimen(position,position_neighbor,r_cut,L): ##This function compute the nondimensional potential energy of the system at the given position #Input: position -- the position of all the particles at this instance # r_cut -- the cutoff for the short-range force field # L -- the size of the simulation cell #Output: np.sum(update_LJ) -- the potential energy of the system at this instance num=position.shape[0] - update_LJ=np.zeros((num-1,1)) + position = np.concatenate((position, position_neighbor),0) + update_LJ=np.zeros((num,1)) #fix value for a certain r_limit dU_drcut=24*r_cut**(-7)-48*r_cut**(-13) U_rcut=4*(r_cut**(-12)-r_cut**(-6)) - for atom in range(num-1): - position_relevent=position[atom:,:] - position_other=position_relevent[1:,:] + for atom in range(num): + # position_relevent=position[atom:,:] + # position_other=position_relevent[1:,:] + position_atom = position[atom,:] + position_other=np.concatenate((position[0:atom,:],position[atom+1:,:]),axis=0) #pbc rule2 - separation=position_relevent[0,:]-position_other + # separation=position_relevent[0,:]-position_other + separation = position_atom - position_other separation_new=pbc2(separation=separation,L=L) r_relat=np.sqrt(np.sum(separation_new**2,axis=1)).reshape(separation_new.shape[0],) LJ=[] #get out the particles inside the r_limit for r0 in r_relat: - if r0 <= r_cut: + if r0 <= r_cut and r0!=0: LJ_num=4*r0**(-12)-4*r0**(-6)-U_rcut-(r0-r_cut)*dU_drcut LJ.append(LJ_num) update_LJ[atom,:]=np.sum(np.array(LJ),axis=0) - return np.sum(update_LJ) + return np.sum(update_LJ)/2 # @numba.njit -def insta_pressure(L,T,position,r_cut,e_scale): +def insta_pressure(L,T,position,position_neighbor,r_cut,e_scale): ##This function computes the dimensionless pressure #Inputs: L -- The size of the simulation cell # T -- The simulation temperature @@ -149,11 +153,14 @@ def insta_pressure(L,T,position,r_cut,e_scale): V=L**3 pres_ideal=num*T*(k_B/e_scale)/V dU_drcut=24*r_cut**(-7)-48*r_cut**(-13) - pres_virial=np.zeros((num-1,1)) - for atom in range(num-1): - position_relevent=position[atom:,:] - position_other=position_relevent[1:,:] - position_atom=position_relevent[0,:] + pres_virial=np.zeros((num,1)) + position = np.concatenate((position,position_neighbor),0) + for atom in range(num): + # position_relevent=position[atom:,:] + # position_other=position_relevent[1:,:] + # position_atom=position_relevent[0,:] + position_atom = position[atom,:] + position_other = np.concatenate((position[0:atom,:],position[atom+1:,:]),axis=0) #pbc rule 2 separation=position_atom-position_other separation_new=pbc2(separation=separation,L=L) @@ -162,7 +169,7 @@ def insta_pressure(L,T,position,r_cut,e_scale): active_r_relat=[] #get out the particles inside the r_limit for r0 in r_relat: - if r0 <= r_cut: + if r0 <= r_cut and r0!=0: #active_r_relat.append(r0) force_num=-(24*r0**(-7)-48*r0**(-13))+dU_drcut force.append(force_num) @@ -171,7 +178,7 @@ def insta_pressure(L,T,position,r_cut,e_scale): active_amount=np.array(active_r_relat).shape[0] rijFij=np.array(active_r_relat).reshape(1,active_amount)@np.array(force).reshape(active_amount,1) pres_virial[atom,:]=rijFij - pres_insta=pres_ideal+np.sum(pres_virial,axis=0)/(3*V) + pres_insta=pres_ideal+np.sum(pres_virial,axis=0)/(3*V)/2 return pres_insta #need to initialize the type before calling the function From 9773febb65c1024ab60602788bfdaeb63180491f Mon Sep 17 00:00:00 2001 From: Hancheng Zhao Date: Fri, 5 Jan 2024 16:13:38 -0500 Subject: [PATCH 8/9] fixed serial bug --- spatial_decompose/MDargon_spatial.py | 338 +++++- .../__pycache__/utils.cpython-310.pyc | Bin 0 -> 8532 bytes .../utils_spatial_decompose.cpython-310.pyc | Bin 8711 -> 8623 bytes spatial_decompose/job.out | 56 + spatial_decompose/job.sh | 7 +- .../argon256_Energy_Temp_Pres1core.csv | 999 ++++++++++++++++++ .../argon256iter1000core16_summary.txt | 2 +- .../results/argon256iter1000core1_summary.txt | 2 +- .../results/argon256iter1000core4_summary.txt | 2 +- spatial_decompose/utils.py | 35 +- spatial_decompose/utils_spatial_decompose.py | 3 - 11 files changed, 1396 insertions(+), 48 deletions(-) create mode 100644 spatial_decompose/__pycache__/utils.cpython-310.pyc diff --git a/spatial_decompose/MDargon_spatial.py b/spatial_decompose/MDargon_spatial.py index 62fadae..52ad443 100644 --- a/spatial_decompose/MDargon_spatial.py +++ b/spatial_decompose/MDargon_spatial.py @@ -2,9 +2,295 @@ import time import copy from LJ_SpatialDecomp import * -import utils_spatial_decompose as ut +# import utils_spatial_decompose as ut +from utils_spatial_decompose import data_saver from mpi4py import MPI +class SpatialDomainData: + #This class creates objects for storing position, velocity and acceleration information + ##This class contain three functions: + ###__init__ (description) + ###__repr__ (description) + ###concat(description) + def __init__(self, position=np.array([]), velocity=np.array([]), acceleration=np.array([])): + self.P = position + self.V = velocity + self.A = acceleration + + def __repr__(self): + return "(P:{}, V:{}, A:{})".format(self.P, self.V, self.A) + + def concat(self, other): + self.P = np.concatenate((self.P, other.P), 0) + self.V = np.concatenate((self.V, other.V), 0) + self.A = np.concatenate((self.A, other.A), 0) + +def LJ_acc(position,neighb_x_0,r_cut,L, rank): + subcube_atoms=position.shape[0] + #careful kind of confusing + position=np.concatenate((position,neighb_x_0),0) + num=position.shape[0] + update_accel=np.zeros((subcube_atoms,3)) + dU_drcut=48*r_cut**(-13)-24*r_cut**(-7) + #for loop is only of subcube we are interested in but we have to account for ALL distance! + for atom in range(subcube_atoms): + position_other=np.concatenate((position[0:atom,:],position[atom+1:num+1,:]),axis=0) + position_atom=position[atom] + separation=position_atom-position_other + separation_new=pbc2(separation=separation,L=L) + r_relat=np.sqrt(np.sum(separation_new**2,axis=1)) + #get out the particles inside the r_cut + accel=np.zeros((r_relat.shape[0],3)) + flag = 0 + for i, r0 in enumerate(r_relat): + if r0 <= r_cut and r0!=0: + separation_active_num=separation_new[i,:] + vector_part=separation_active_num*(1/r0) + scalar_part=48*r0**(-13)-24*r0**(-7)-dU_drcut + accel_num=vector_part*scalar_part + accel[i,:]=accel_num + # if np.abs(position_atom[0]-4.641496)<0.001 and np.abs(position_atom[1]-3.092705)<0.001 and np.abs(position_atom[2]-3.090466)<0.001: + # flag = 1 + # print(position_atom, accel_num, r0) + update_accel[atom,:]=np.sum(accel,axis=0) + # if np.abs(update_accel[atom,:][0]+6.2848242)<1e-4: + # print('update accel',update_accel[atom,:]) + # print(accel[accel.any(axis=1)],r_relat[accel.any(axis=1)]) + return update_accel.reshape(subcube_atoms,3) + +def pbc1(position,L): + ##This function perform the first rule of periodic boundary condition + #Input: position -- the position before PBC1 + # L -- the simulation cell size + #Ouput: x_new -- the updated position after PBC1 + position_new=np.zeros((position.shape[0],3)) + for i in range(position.shape[0]): + position_ind=position[i,:] + position_empty=np.zeros((1,3)) + for j in range(3): + # position_axis=numba.float64(position_ind[j]) + position_axis = position_ind[j] + if position_axis < 0: + position_axis_new=position_axis+L + elif position_axis >= L: + position_axis_new=position_axis-L + else: + position_axis_new=position_axis + position_empty[:,j]=position_axis_new + position_new[i,:]=position_empty + return position_new + +# @numba.njit +def pbc2(separation,L): + ##This function perform the second rule of periodic boundary condition + #Input: separation -- separation before PBC2 + # L -- the simulation cell size + #Ouput: separation_new -- the updated separation after PBC2 + separation_new=np.zeros((separation.shape[0],3)) + for i in range(separation.shape[0]): + separation_ind=separation[i,:] + separation_empty=np.zeros((1,3)) + for j in range(3): + # separation_axis=numba.float64(separation_ind[j]) + separation_axis = separation_ind[j] + if separation_axis < -L/2: + separation_axis_new=separation_axis+L + elif separation_axis >= L/2: + separation_axis_new=separation_axis-L + else: + separation_axis_new=separation_axis + separation_empty[:,j]=separation_axis_new + separation_new[i,:]=separation_empty + return separation_new + +def separate_points(infodict, my_rank, nproc): + neighb_spd = None + # Processor matrix n*n*1 (for comparison with force decomposition) + axis = np.sqrt(nproc) + # Here we need to be careful about only copying the neighboring subcube + x,y,z = my_rank % axis, my_rank / axis, 0 + x,y,z = int(np.floor(x)), int(np.floor(y)), int(np.floor(z)) + x_mesh,y_mesh = np.meshgrid(np.linspace(x-1,x+1,3),np.linspace(y-1,y+1,3)) + neighbor_xy = np.column_stack((x_mesh.ravel(),y_mesh.ravel())) + # neighbor_rank = np.array([[i-5,i-4,i-3],[i-1,i,i+1],[i+3,i+4,i+5]]) + # for row in neighbor_rank: + # for col in row: + # if np.floor(col / world) != np.floor(row[1] / world): + # col = np.floor(col / world) * world + world + if axis<=3: + neighbor_rank = np.arange(0,nproc,1) + else: + neighbor_rank = np.zeros(9) + for t,xy in enumerate(neighbor_xy): + xy_old = xy.copy() + if xy[0]<0: + xy[0] = xy[0] + axis + if xy[0]==axis: + xy[0] = xy[0] - axis + # elif xy[0]==axis and xy[1]=axis-1: + # xy[0] = xy[0] - axis + # xy[1] = 0 + if xy[1]<0: + xy[1] = xy[1] + axis + if xy[1] == axis: + xy[1] = xy[1] - axis + # xy[0] = xy[0] + # print(xy_old,xy) + # for i in xy: + # if i<0: + # i = i + axis + # elif i == axis: + # i = i - axis + neighbor_rank[t] = (xy[0] + xy[1]*axis) + # print('neighboring ',my_rank, (x,y), neighbor_rank) + + # copy the info in neighboring ranks + for i, spd in infodict.items(): + if i!=my_rank and i in neighbor_rank: + if neighb_spd is None: + neighb_spd = copy.deepcopy(spd) + else: + neighb_spd.concat(spd) + return infodict[my_rank], neighb_spd + +def cell_to_dict(info,nx,ny,nz,L): + ##This is the helper function to create dictionary containing matrix for cell_to_obj + #Inpust: info -- the position + velocity + acceleration of the patricles at the + # cell_dict = Dict.empty(key_type=types.int64, value_type=float_array) + cell_dict = {} + xinterval=L/nx + yinterval=L/ny + zinterval=L/nz + # print('interval ', xinterval, yinterval) + #cell_lists={} + for i in range(nx*ny*nz): + cell_dict[i]= np.zeros((1,9)) + for i in range(info.shape[0]): + atom=info[i,0:9].reshape(1,9) + #check extra one!!! + #if statements !!!!!!! + #check later + # atomID=int(((np.floor(atom[:,0]/xinterval)+(np.floor(atom[:,1]/yinterval))*ny)+(np.floor(atom[:,2]/zinterval))*(nx*ny))[0]) + atomID=int(((np.floor(atom[:,0]/xinterval)+(np.floor(atom[:,1]/yinterval))*ny))[0]) + cell_dict[atomID]=np.append(cell_dict[atomID],atom,axis=0) + for i in range(nx*ny*nz): + cell_dict[i]=cell_dict[i][1:,:] + return cell_dict + +def cell_to_obj(positions,nx,ny,nz,L): + cell_lists=cell_to_dict(positions,nx,ny,nz,L) + new_cell_list={} + for i in range(nx*ny*nz): + # I think this works but we should think more about what an "empty" shape means + # currently when a key points to an empty cube the cube has a position vector of dimensions [0,3] + if cell_lists[i].shape[0]!=0: + temp_reshaped=cell_lists[i] + temp_position = temp_reshaped[:,0:3] + assert(temp_position.shape[1] == 3) + temp_velocity = temp_reshaped[:,3:6] + temp_acceleration = temp_reshaped[:,6:9] + spatial_domain_data = SpatialDomainData(temp_position, + temp_velocity, + temp_acceleration) + new_cell_list[i] = spatial_domain_data + else: + new_cell_list[i] = SpatialDomainData(np.empty((0,3)), + np.empty((0,3)), + np.empty((0,3))) + return new_cell_list + +def Kin_Eng(velocity): + ##This function compute the average kinetic energy of the system at given the velocity + #Input: velocity -- the velocities of all the particles + #Output: Kinetic_sum -- the average kinetic energy of the system + num=velocity.shape[0] + Kinetic_per=0.5*np.sum(velocity**2,axis=1) + Kinetic_avg=np.sum(Kinetic_per,axis=0) + return Kinetic_avg + +def LJ_potent_nondimen(position,position_neighbor,r_cut,L): + ##This function compute the nondimensional potential energy of the system at the given position + #Input: position -- the position of all the particles at this instance + # r_cut -- the cutoff for the short-range force field + # L -- the size of the simulation cell + #Output: np.sum(update_LJ) -- the potential energy of the system at this instance + num=position.shape[0] + position = np.concatenate((position, position_neighbor),0) + update_LJ=np.zeros((num,1)) + #fix value for a certain r_limit + dU_drcut=24*r_cut**(-7)-48*r_cut**(-13) + U_rcut=4*(r_cut**(-12)-r_cut**(-6)) + for atom in range(num): + # position_relevent=position[atom:,:] + # position_other=position_relevent[1:,:] + position_atom = position[atom,:] + position_other=np.concatenate((position[0:atom,:],position[atom+1:,:]),axis=0) + #pbc rule2 + # separation=position_relevent[0,:]-position_other + separation = position_atom - position_other + separation_new=pbc2(separation=separation,L=L) + r_relat=np.sqrt(np.sum(separation_new**2,axis=1)).reshape(separation_new.shape[0],) + LJ=[] + #get out the particles inside the r_limit + for r0 in r_relat: + if r0 <= r_cut and r0!=0: + LJ_num=4*r0**(-12)-4*r0**(-6)-U_rcut-(r0-r_cut)*dU_drcut + LJ.append(LJ_num) + update_LJ[atom,:]=np.sum(np.array(LJ),axis=0) + return np.sum(update_LJ)/2 + +def insta_pressure(L,T,position,position_neighbor,r_cut,e_scale): + ##This function computes the dimensionless pressure + #Inputs: L -- The size of the simulation cell + # T -- The simulation temperature + # position -- The position of all the particles at this time step + # e_scale -- The energy scale of this particles + #Ouputs: pres_insta -- The instant pressure at this moment + num=position.shape[0] + k_B=1.38064852*10**(-23) + V=L**3 + pres_ideal=num*T*(k_B/e_scale)/V + dU_drcut=24*r_cut**(-7)-48*r_cut**(-13) + pres_virial=np.zeros((num,1)) + position = np.concatenate((position,position_neighbor),0) + for atom in range(num): + # position_relevent=position[atom:,:] + # position_other=position_relevent[1:,:] + # position_atom=position_relevent[0,:] + position_atom = position[atom,:] + position_other = np.concatenate((position[0:atom,:],position[atom+1:,:]),axis=0) + #pbc rule 2 + separation=position_atom-position_other + separation_new=pbc2(separation=separation,L=L) + r_relat=np.sqrt(np.sum(separation_new**2,axis=1)).reshape(separation_new.shape[0],) + force=[] + active_r_relat=[] + #get out the particles inside the r_limit + for r0 in r_relat: + if r0 <= r_cut and r0!=0: + #active_r_relat.append(r0) + force_num=-(24*r0**(-7)-48*r0**(-13))+dU_drcut + force.append(force_num) + active_r_relat.append(r0) + #get out the particles inside the r_cut + active_amount=np.array(active_r_relat).shape[0] + rijFij=np.array(active_r_relat).reshape(1,active_amount)@np.array(force).reshape(active_amount,1) + pres_virial[atom,:]=rijFij + pres_insta=pres_ideal+np.sum(pres_virial,axis=0)/(3*V)/2 + return pres_insta + +def concatDict(infodict): + wholeDict=None + for i,spd in infodict.items(): + if(wholeDict is None): + wholeDict = copy.deepcopy(spd) + else: + wholeDict.concat(spd) + return wholeDict + # MPI initialize comm = MPI.COMM_WORLD rank = comm.Get_rank() @@ -49,8 +335,8 @@ # info[0,:,:]=np.concatenate((position_init,x_dot_init,a_init),axis=1) info[0,:,:] = info_init # np.savetxt('../data/init.txt',info[0,:,:],fmt='%.6f') - infotodic=ut.cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L0) - KE[0,:] = ut.Kin_Eng(info[0,:,3:6]) + infotodic=cell_to_obj((info[0,:,:]),subdiv[0],subdiv[1],subdiv[2],L0) + KE[0,:] = Kin_Eng(info[0,:,3:6]) T_insta[0,:]=2*KE[0,:]*energy_scale/(3*(size_sim-1)*k_B) #k print(T_insta[0,:][0]) else: @@ -59,10 +345,10 @@ infotodic = comm.bcast(infotodic, root = 0) T_single = comm.bcast(T_insta[0,:][0], root=0) -my_spd, neighs_spd = ut.separate_points(infotodic, my_rank = rank, nproc = size) +my_spd, neighs_spd = separate_points(infotodic, my_rank = rank, nproc = size) #zero step value -PE_single=ut.LJ_potent_nondimen(my_spd.P,neighs_spd.P,r_cut=r_c,L=L0) -P_single=ut.insta_pressure(L0,T_single,my_spd.P,neighs_spd.P,r_c,energy_scale) #unitless +PE_single=LJ_potent_nondimen(my_spd.P,neighs_spd.P,r_cut=r_c,L=L0) +P_single=insta_pressure(L0,T_single,my_spd.P,neighs_spd.P,r_c,energy_scale) #unitless PE_all = comm.reduce(PE_single,op=MPI.SUM,root=0) P_all = comm.reduce(P_single,op=MPI.SUM,root=0) @@ -72,18 +358,24 @@ # Run MD for step in range(stop_step): - my_spd_send=utp.vel_Ver( - comm = comm, - infodict=infotodic, - dt=dt, - r_limit=r_c, - L=L0, - my_rank=rank - ) + my_spd, neighs_spd=separate_points(infotodic, rank, size) + my_spd.A = LJ_acc(position=my_spd.P,neighb_x_0=neighs_spd.P,r_cut=r_c,L=L0,rank=rank) + my_spd.V = my_spd.V + my_spd.A*(dt) + my_spd.P = my_spd.P + my_spd.V * dt + my_spd.P = pbc1(position=my_spd.P,L=L0) + # my_spd_send=utp.vel_Ver( + # comm = comm, + # infodict=infotodic, + # dt=dt, + # r_limit=r_c, + # L=L0, + # my_rank=rank + # ) + my_spd_send = (rank,my_spd) # apply periodic boundary condition - my_spd_send[1].P = ut.pbc1(my_spd_send[1].P,L=L0) + # my_spd_send[1].P = ut.pbc1(my_spd_send[1].P,L=L0) #calculate and store KE in parallel - KE_single = ut.Kin_Eng(my_spd_send[1].V) + KE_single = Kin_Eng(my_spd_send[1].V) # gather temp_infodict=comm.gather(my_spd_send,root=0) @@ -96,12 +388,12 @@ print('current time step is ', step) temp_infodict=list(filter(None, temp_infodict)) info_temp=dict(temp_infodict) - tmp=ut.concatDict(info_temp) - info[step+1,:,:]=np.concatenate((tmp.P,tmp.V,tmp.A),1) + tmp = concatDict(info_temp) + info[step+1,:,:] = np.concatenate((tmp.P,tmp.V,tmp.A),1) # info[step+1,:,:] = np.round(info[step+1,:,:],4) # info[step+1,:,0:3] = ut.pbc1(info[step+1,:,0:3],L=L0) #UPDATE CUBES MAKE SURE ATOMS ARE IN RIGHT CUBES - infotodic=ut.cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) + infotodic = cell_to_obj(info[step+1,:,:],subdiv[0],subdiv[1],subdiv[2],L0) # gather KE and T KE[step+1,:]=KE_all T_insta[step+1,:]=2*KE_all*energy_scale/(3*(size_sim-1)*k_B) #k @@ -109,9 +401,9 @@ infotodic = comm.bcast(infotodic, root = 0) T_single = comm.bcast(T_insta[step+1,:][0], root = 0) # calculate PE,P in parallel - my_spd, neighs_spd = ut.separate_points(infotodic, my_rank = rank, nproc = size) - PE_single = ut.LJ_potent_nondimen(position = my_spd.P, position_neighbor = neighs_spd.P, r_cut = r_c, L=L0) - P_single = ut.insta_pressure(L0,T_single,my_spd.P,neighs_spd.P,r_c,energy_scale) + my_spd, neighs_spd = separate_points(infotodic, my_rank = rank, nproc = size) + PE_single = LJ_potent_nondimen(position = my_spd.P, position_neighbor = neighs_spd.P, r_cut = r_c, L=L0) + P_single = insta_pressure(L0,T_single,my_spd.P,neighs_spd.P,r_c,energy_scale) # gather back to 0 PE_all = comm.reduce(PE_single,op=MPI.SUM,root=0) P_all = comm.reduce(P_single,op=MPI.SUM,root=0) @@ -130,7 +422,7 @@ KE = np.round(KE,4) T_insta = np.round(T_insta,4) P_insta = np.round(P_insta,4) - ut.data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, size, False) + data_saver(info, PE, KE, T_insta, P_insta, L0, num_atoms,part_type,name,period, stop_step, r_c, size, False) comm.barrier() # if rank==0: diff --git a/spatial_decompose/__pycache__/utils.cpython-310.pyc b/spatial_decompose/__pycache__/utils.cpython-310.pyc new file mode 100644 index 0000000000000000000000000000000000000000..d0e0ed7bc9d397a9a2b46256c7e585811012f1d6 GIT binary patch literal 8532 zcmeHMOKc>^dG6}h^z=M991frR&`40C9YqmWQfvvEg<@qNj`bim-j$pXmK(iOP4190 z)5Gc}MNVn}LDV9MlZA5#VqcPwKyuhi5WsgIa?3rZIvEI%gvc=uAci6N`>T6~L(+=~ 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@@ -60,7 +61,8 @@ def pbc2(separation,L): separation_ind=separation[i,:] separation_empty=np.zeros((1,3)) for j in range(3): - separation_axis=numba.float64(separation_ind[j]) + # separation_axis=numba.float64(separation_ind[j]) + separation_axis = separation_ind[j] if separation_axis < -L/2: separation_axis_new=separation_axis+L elif separation_axis > L/2: @@ -71,7 +73,7 @@ def pbc2(separation,L): separation_new[i,:]=separation_empty return separation_new -@numba.njit +# @numba.njit def random_vel_generator(n,T_equal,e_scale): ##This function generate random initial velocity at the desired temperature #Input: n -- number of atoms @@ -95,7 +97,7 @@ def random_vel_generator(n,T_equal,e_scale): vel_per_particle=vel_per_particle*scaling_ratio return vel_per_particle -@numba.njit +# @numba.njit def Kin_Eng(velocity): ##This function compute the average kinetic energy of the system at given the velocity #Input: velocity -- the velocities of all the particles @@ -105,7 +107,7 @@ def Kin_Eng(velocity): Kinetic_avg=np.sum(Kinetic_per,axis=0) return Kinetic_avg -@numba.njit +# @numba.njit def LJ_potent_nondimen(position,r_cut,L): ##This function compute the nondimensional potential energy of the system at the given position #Input: position -- the position of all the particles at this instance @@ -133,7 +135,7 @@ def LJ_potent_nondimen(position,r_cut,L): update_LJ[atom,:]=np.sum(np.array(LJ),axis=0) return np.sum(update_LJ) -@numba.njit +# @numba.njit def insta_pressure(L,T,position,r_cut,e_scale): ##This function computes the dimensionless pressure #Inputs: L -- The size of the simulation cell @@ -172,12 +174,13 @@ def insta_pressure(L,T,position,r_cut,e_scale): return pres_insta #need to initialize the type before calling the function -float_array = types.float64[:,:] -@numba.njit() +# float_array = types.float64[:,:] +# @numba.njit() def cell_to_dict(info,nx,ny,nz,L): ##This is the helper function to create dictionary containing matrix for cell_to_obj #Inpust: info -- the position + velocity + acceleration of the patricles at the - cell_dict = Dict.empty(key_type=types.int64, value_type=float_array) + # cell_dict = Dict.empty(key_type=types.int64, value_type=float_array) + cell_dict = {} xinterval=L/nx yinterval=L/ny zinterval=L/nz diff --git a/spatial_decompose/utils_spatial_decompose.py b/spatial_decompose/utils_spatial_decompose.py index 3d7e724..218148e 100644 --- a/spatial_decompose/utils_spatial_decompose.py +++ b/spatial_decompose/utils_spatial_decompose.py @@ -43,7 +43,6 @@ def pbc1(position,L): if position_axis < 0: position_axis_new=position_axis+L elif position_axis >= L: - print(position_axis) position_axis_new=position_axis-L else: position_axis_new=position_axis @@ -203,8 +202,6 @@ def cell_to_dict(info,nx,ny,nz,L): #check later # atomID=int(((np.floor(atom[:,0]/xinterval)+(np.floor(atom[:,1]/yinterval))*ny)+(np.floor(atom[:,2]/zinterval))*(nx*ny))[0]) atomID=int(((np.floor(atom[:,0]/xinterval)+(np.floor(atom[:,1]/yinterval))*ny))[0]) - if atomID>15: - print(atomID,atom, atom[:,0][0]==L) cell_dict[atomID]=np.append(cell_dict[atomID],atom,axis=0) for i in range(nx*ny*nz): cell_dict[i]=cell_dict[i][1:,:] From 719d1a8ad3aaeb4384ab61daa3637de51247fcdc Mon Sep 17 00:00:00 2001 From: Hancheng Zhao Date: Fri, 5 Jan 2024 16:45:15 -0500 Subject: [PATCH 9/9] 9 cores --- spatial_decompose/job.out | 15 +- spatial_decompose/job.sh | 2 +- .../argon256_Energy_Temp_Pres36core.csv | 1002 +++++++++++++++++ .../argon256_Energy_Temp_Pres9core.csv | 1002 +++++++++++++++++ .../results/argon256iter1000core36.txt | 256 +++++ .../argon256iter1000core36_summary.txt | 6 + .../results/argon256iter1000core9.txt | 256 +++++ .../results/argon256iter1000core9_summary.txt | 6 + 8 files changed, 2539 insertions(+), 6 deletions(-) create mode 100644 spatial_decompose/results/argon256_Energy_Temp_Pres36core.csv create mode 100644 spatial_decompose/results/argon256_Energy_Temp_Pres9core.csv create mode 100644 spatial_decompose/results/argon256iter1000core36.txt create mode 100644 spatial_decompose/results/argon256iter1000core36_summary.txt create mode 100644 spatial_decompose/results/argon256iter1000core9.txt create mode 100644 spatial_decompose/results/argon256iter1000core9_summary.txt diff --git a/spatial_decompose/job.out b/spatial_decompose/job.out index d506442..0438a86 100644 --- a/spatial_decompose/job.out +++ b/spatial_decompose/job.out @@ -1,8 +1,13 @@ /opt/intel/oneapi/intelpython/latest/bin/mpirun -0 4 -2 4 -3 4 -1 4 +6 9 +1 9 +3 9 +4 9 +7 9 +2 9 +5 9 +8 9 +0 9 123.00000045477438 current time step is 0 current time step is 20 @@ -54,4 +59,4 @@ current time step is 920 current time step is 940 current time step is 960 current time step is 980 -Run time is 341.940 seconds +Run time is 180.458 seconds diff --git a/spatial_decompose/job.sh b/spatial_decompose/job.sh index 3c7baf4..cb916f8 100644 --- a/spatial_decompose/job.sh +++ b/spatial_decompose/job.sh @@ -1,6 +1,6 @@ #!/bin/bash #SBATCH -N 1 -#SBATCH -n 4 +#SBATCH -n 9 #SBATCH -p RM-small #SBATCH --mem-per-cpu=2000M #SBATCH -e job.err diff --git a/spatial_decompose/results/argon256_Energy_Temp_Pres36core.csv b/spatial_decompose/results/argon256_Energy_Temp_Pres36core.csv new file mode 100644 index 0000000..886d93f --- /dev/null +++ b/spatial_decompose/results/argon256_Energy_Temp_Pres36core.csv @@ -0,0 +1,1002 @@ +step,KE,PE,T_insta,P_insta +0,391.3016,-412.9481,123.0,4.6835 +1,391.1711,-412.3081,122.959,4.6955 +2,390.2421,-410.9737,122.667,4.7172 +3,388.5035,-408.8307,122.1205,4.7503 +4,385.9581,-405.8835,121.3204,4.7946 +5,382.6121,-402.1395,120.2686,4.8499 +6,378.4746,-397.6103,118.968,4.9159 +7,373.5592,-392.3112,117.4229,4.9922 +8,367.8836,-386.263,115.6389,5.0787 +9,361.4716,-379.4925,113.6234,5.1745 +10,354.3533,-372.0334,111.3858,5.2793 +11,346.5663,-363.9277,108.9381,5.3922 +12,338.157,-355.2262,106.2948,5.5125 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a/spatial_decompose/results/argon256iter1000core9_summary.txt b/spatial_decompose/results/argon256iter1000core9_summary.txt new file mode 100644 index 0000000..9999bd6 --- /dev/null +++ b/spatial_decompose/results/argon256iter1000core9_summary.txt @@ -0,0 +1,6 @@ +Simulation Cell Size(unitless): 6.8 +Simulation Particles Amount: 256 +File Name: argon256 +Simulation Time: 180.4576563835144 +Simulation Step: 1000 +Force Cut-off: 1.6