From 4b333c17b01f6099ca4b1a569f24a70ff27eda85 Mon Sep 17 00:00:00 2001
From: RexWight <rexjared86@gmail.com>
Date: Mon, 26 May 2025 11:28:52 -0600
Subject: [PATCH 1/4] dir changed

---
 src/scripts/NS.jl | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/scripts/NS.jl b/src/scripts/NS.jl
index 87f34fc..34d6f6d 100644
--- a/src/scripts/NS.jl
+++ b/src/scripts/NS.jl
@@ -1,6 +1,5 @@
 
-
-cd("/Users/legoses/OneDrive - BYU-Idaho/codes/MatSim/src/libraries/")
+cd("C:\\Users\\rexja\\OneDrive - BYU-Idaho\\Classes\\Nelson Research Group\\MatSim.jl\\src\\libraries")
 push!(LOAD_PATH,pwd())
 
 using ase

From 1746eb61ebf8b7e951c482046592e3cc13f075ef Mon Sep 17 00:00:00 2001
From: RexWight <rexjared86@gmail.com>
Date: Sat, 7 Jun 2025 14:41:10 -0600
Subject: [PATCH 2/4] Output files changed but not updated:

---
 src/scripts/NS-Rexs-Laptop.jl  |  73 ++++++++++++
 src/scripts/NS-Rexs-Laptop.out | 104 +++++++++++++++++
 src/scripts/NS.jl              |   2 +-
 src/scripts/NS.out             | 200 ++++++++++++++++-----------------
 4 files changed, 278 insertions(+), 101 deletions(-)
 create mode 100644 src/scripts/NS-Rexs-Laptop.jl
 create mode 100644 src/scripts/NS-Rexs-Laptop.out

diff --git a/src/scripts/NS-Rexs-Laptop.jl b/src/scripts/NS-Rexs-Laptop.jl
new file mode 100644
index 0000000..7603233
--- /dev/null
+++ b/src/scripts/NS-Rexs-Laptop.jl
@@ -0,0 +1,73 @@
+
+
+cDir = @__DIR__
+cd(cDir)
+push!(LOAD_PATH,joinpath(cDir,"../libraries"))
+#cd("C:\\Users\\rexja\\OneDrive - BYU-Idaho\\Classes\\Nelson Research Group\\MatSim.jl\\src\\libraries")
+push!(LOAD_PATH,pwd())
+
+using ase
+using LennardJones
+using nSampling
+using YAML
+
+# Initialize the model
+resultsPath = joinpath(cDir,"draws-LJ.Pt-Ag")
+
+# Build model with averages of the draws for fit parameters.
+LJ_average = LennardJones.get_LJ_averages(resultsPath)
+input = YAML.load_file(joinpath(cDir,"NS.yml"))
+myNS = nSampling.initialize(input["params"],LJ_average);# Initialize the simulation...
+nSampling.tune_step_sizes!(myNS,LJ_average)
+nSampling.run_NS(myNS,LJ_average)
+
+
+# Disregard all below
+# display(ase.eval_KE(myNS.walkers[sEnergies[end-3]]))
+# println(myNS.walkers[sEnergies[end-3]].coordSys)
+# myNS.walkers[4].lj_vec
+# ase.eval_forces(myNS.walkers[1],LJ_average)
+# display(ase.get_neighbor_distances(myNS.walkers[1],4.0))
+# println(myNS.walker_params.MD_time_step)
+# nSampling.tune_step_sizes(myNS.walkers[sEnergies[end-2]],myNS.walker_params,LJ_average,E_max)
+
+# ase.eval_KE(myNS.walkers[4])
+# sum(0.5 * [x' * x for x in myNS.walkers[4].velocities])
+# nSampling.run_NS(myNS,LJ_average)
+# check =ase.get_nn_list(myNS.walkers[2],5.6)
+# check = myNS.walkers[1].positions
+# myvec = ["ab", "dc", "ef"]
+# !("ab" in myvec)
+# println(myNS.walkers[1].lVecs)
+# println(ase.cell_volume(myNS.walkers[1]))
+# ase.DirectToCartesian!(myNS.walkers[1])
+# myNS.walker_params.MD_time_step = 0.000001
+# ase.do_MD!(myNS.walkers[3],LJ_average,myNS.walker_params,E_max)
+# 2 .* check #.* [2 * 5.0 ./ x for x in check] #.* 2 .* check
+# [2 * 5.0 ./ x for x in check] #.* 2 .* check
+# print(myNS.walkers[5].positions)
+# begin_energy = ase.eval_energy(myNS.walkers[2],LJ_average)
+# using Plots
+# using StaticArrays
+# using LinearAlgebra
+# nSampling.walk_single_walker!(myNS.walkers[2],LJ_average,myNS.walker_params,ase.eval_energy(myNS.walkers[2],LJ_average))
+# display(ase.eval_energy(myNS.walkers[2],LJ_average))
+# ase.gradientForce(LJ_average,myNS.walkers[2],@SVector[1,4],@SVector[2,2,2])
+# println(myNS.walkers[2].fitEnergy)
+# display(myNS.walkers[2].lVecs)
+# display(myNS.walkers[2].atomicBasis)
+# ase.mapIntoCell(myNS.walkers[2])
+# ase.DirectToCartesian!(myNS.walkers[2])
+
+# using LinearAlgebra
+# nHat = [[norm(x) > 0.0 ? x / norm(x) : x for x in y] for y in myNS.walkers[2].atomicBasis ]
+
+# any([isnan(z) for x in myNS.walkers[2].atomicBasis for y in x for z in y])
+# any(isnan.(myNS.walkers[2].atomicBasis[1]))
+# floor(-0.5)
+# rand(1:5)
+# #nSampling.GMC(myNS.configs[55],500,LJ_average)
+# nSampling.run_NS(myNS,LJ_average)
+# rands = nSampling.get_random_displacements([2,3])
+
+# println(rands[2])
\ No newline at end of file
diff --git a/src/scripts/NS-Rexs-Laptop.out b/src/scripts/NS-Rexs-Laptop.out
new file mode 100644
index 0000000..ce3f7d7
--- /dev/null
+++ b/src/scripts/NS-Rexs-Laptop.out
@@ -0,0 +1,104 @@
+N_walkers = 20
+N_cull = 6
+N_steps_per_walker = 2000
+eps = 0.001
+0.5102040816326531 228.5086919268981 
+0.3644314868804665 215.85392369019976 
+0.2603082049146189 208.75774286857677 
+0.18593443208187066 192.21386373643966 
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+0.09486450616421974 189.70694892353316 
+0.06776036154587124 189.1005179403787 
+0.04840025824705089 177.15326974066213 
+0.03457161303360778 167.60681101493745 
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+1.3117063185560345e-14 95.51049752226578 
+9.369330846828818e-15 95.13256252634817 
+6.692379176306299e-15 94.6834582255137 
+4.780270840218785e-15 94.45229511491479 
+3.4144791715848464e-15 94.33558529693632 
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+1.7420812099922686e-15 93.98646473549903 
diff --git a/src/scripts/NS.jl b/src/scripts/NS.jl
index e42ef56..82df88e 100644
--- a/src/scripts/NS.jl
+++ b/src/scripts/NS.jl
@@ -3,7 +3,7 @@
 cDir = @__DIR__
 cd(cDir)
 push!(LOAD_PATH,joinpath(cDir,"../libraries"))
-cd("C:\\Users\\rexja\\OneDrive - BYU-Idaho\\Classes\\Nelson Research Group\\MatSim.jl\\src\\libraries")
+#cd("C:\\Users\\rexja\\OneDrive - BYU-Idaho\\Classes\\Nelson Research Group\\MatSim.jl\\src\\libraries")
 push!(LOAD_PATH,pwd())
 
 using ase
diff --git a/src/scripts/NS.out b/src/scripts/NS.out
index 44c1594..fa2a3c5 100644
--- a/src/scripts/NS.out
+++ b/src/scripts/NS.out
@@ -2,103 +2,103 @@ N_walkers = 20
 N_cull = 6
 N_steps_per_walker = 2000
 eps = 0.001
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From 5724182bf71598b3ff285270ee59efbdb9605485 Mon Sep 17 00:00:00 2001
From: RexWight <rexjared86@gmail.com>
Date: Wed, 11 Jun 2025 15:01:27 -0600
Subject: [PATCH 3/4] My edited files

---
 src/libraries/nSampling.jl          |   98 +--
 src/my_files/Figure_1.png           |  Bin 0 -> 29588 bytes
 src/my_files/NS.out                 | 1004 +++++++++++++++++++++++++++
 src/my_files/Super_computer-500.png |  Bin 0 -> 30378 bytes
 src/my_files/time.py                |   21 +
 src/scripts/NS-Rexs-Laptop.jl       |   73 --
 src/scripts/NS-Rexs-Laptop.out      |  104 ---
 src/scripts/NS.out                  |  300 +++++---
 src/scripts/NS.yml                  |    2 +-
 9 files changed, 1276 insertions(+), 326 deletions(-)
 create mode 100644 src/my_files/Figure_1.png
 create mode 100644 src/my_files/NS.out
 create mode 100644 src/my_files/Super_computer-500.png
 create mode 100644 src/my_files/time.py
 delete mode 100644 src/scripts/NS-Rexs-Laptop.jl
 delete mode 100644 src/scripts/NS-Rexs-Laptop.out

diff --git a/src/libraries/nSampling.jl b/src/libraries/nSampling.jl
index 83c4787..a996fa0 100755
--- a/src/libraries/nSampling.jl
+++ b/src/libraries/nSampling.jl
@@ -327,7 +327,7 @@ function reverse_sort_energies(NS)
 end
 
 function run_NS(NS::NS,LJ::LennardJones.model)
-
+    println("Reading the file")
     V = (NS.n_walkers - NS.n_cull + 1)/(NS.n_walkers + 1)
     cDir = pwd()
 
@@ -339,56 +339,58 @@ function run_NS(NS::NS,LJ::LennardJones.model)
     write(io, "eps = " * string(NS.eps) * "\n")
     perms = zeros(MVector{length(NS.walkers),Int})
 #    while V > NS.eps
-    for i= 1:100
-        println(i)
-        println("V = ", V)
-        ## Find the top Kr highest energies
-        
-        sortperm!(perms,[i.energies[2] for i in NS.walkers])  # 4 allocations
-        perms = reverse(perms) # 1 allocation
-        #perms =  reverse(sortperm([i.energies[2] for i in NS.walkers]))
-       # println(sort([i.energyPerAtomModel for i in NS.walkers]))
-        E_max = NS.walkers[perms[NS.n_cull]].energies[2]  # 3 allocations
-        # Which configs need to be thrown out.
-        forDelete = perms[1:NS.n_cull]  # 2 allocations
-        # Which configs can be kept
-        keeps = perms[NS.n_cull + 1: end]  # 2 allocations
-        println("Energy cutoff")
-        display(E_max)
-        println("PE: ", ase.eval_energy(NS.walkers[perms[NS.n_cull]],LJ,do_KE = false))
-        println("KE: ", ase.eval_KE(NS.walkers[perms[NS.n_cull]]))
-        println("Total: ", ase.eval_energy(NS.walkers[perms[NS.n_cull]],LJ))
-
-        if i %12 == 0  # 12 is pretty arbitrary.. Need a better way to see if need to re-tune
-            println("Stopping to retune step sizes")
-            energies_before = [ase.eval_energy(walker, LJ, force_recalc = true) for walker in NS.walkers]
-            tune_step_sizes!(NS,LJ)
-            energies_after = [ase.eval_energy(walker, LJ, force_recalc = true) for walker in NS.walkers]
-            if !isapprox(energies_before,energies_after, atol=1e-5)
-                error("tune step sizes changed configurations")
+    for i= 1:500
+        elapsed = @elapsed begin 
+            println(i)
+            println("V = ", V)
+            ## Find the top Kr highest energies
+            
+            sortperm!(perms,[i.energies[2] for i in NS.walkers])  # 4 allocations
+            perms = reverse(perms) # 1 allocation
+            #perms =  reverse(sortperm([i.energies[2] for i in NS.walkers]))
+        # println(sort([i.energyPerAtomModel for i in NS.walkers]))
+            E_max = NS.walkers[perms[NS.n_cull]].energies[2]  # 3 allocations
+            # Which configs need to be thrown out.
+            forDelete = perms[1:NS.n_cull]  # 2 allocations
+            # Which configs can be kept
+            keeps = perms[NS.n_cull + 1: end]  # 2 allocations
+            println("Energy cutoff")
+            display(E_max)
+            println("PE: ", ase.eval_energy(NS.walkers[perms[NS.n_cull]],LJ,do_KE = false))
+            println("KE: ", ase.eval_KE(NS.walkers[perms[NS.n_cull]]))
+            println("Total: ", ase.eval_energy(NS.walkers[perms[NS.n_cull]],LJ))
+
+            if i %12 == 0  # 12 is pretty arbitrary.. Need a better way to see if need to re-tune
+                println("Stopping to retune step sizes")
+                energies_before = [ase.eval_energy(walker, LJ, force_recalc = true) for walker in NS.walkers]
+                tune_step_sizes!(NS,LJ)
+                energies_after = [ase.eval_energy(walker, LJ, force_recalc = true) for walker in NS.walkers]
+                if !isapprox(energies_before,energies_after, atol=1e-5)
+                    error("tune step sizes changed configurations")
+                end
+                println("Done with tune up------------------------------------------------->")
             end
-            println("Done with tune up------------------------------------------------->")
-        end
-#        display(E_max - ase.eval_KE(NS.walkers[perms[NS.n_cull]]))
-        for replace_walker in forDelete
-            #Copy one of the configs that didn't get thrown out as the starting point
-            #println("Initializing random walk to replace configuration ", i)
-            #display(sample(keeps))
-            NS.walkers[replace_walker] = deepcopy(NS.walkers[sample(keeps,1)[1]])  # ~ 50 allocations
-            #println("E-max for this walker: ", E_max)
-            #println("Starting energy of this walker: (should be lower than E-max)", ase.eval_energy(NS.walkers[replace_walker],LJ,force_recalc = true))
-            walk_single_walker!(NS.walkers[replace_walker],LJ,NS.walker_params,E_max)
-            #return nothing            
-            #println("Ending energy of this walker: (should be lower than E-max)", ase.eval_energy(NS.walkers[replace_walker],LJ,force_recalc = true))
-#            randomWalk!(NS.walkers[replace_walker],LJ,energyCutoff,NS.n_iter)
+    #        display(E_max - ase.eval_KE(NS.walkers[perms[NS.n_cull]]))
+            for replace_walker in forDelete
+                #Copy one of the configs that didn't get thrown out as the starting point
+                #println("Initializing random walk to replace configuration ", i)
+                #display(sample(keeps))
+                NS.walkers[replace_walker] = deepcopy(NS.walkers[sample(keeps,1)[1]])  # ~ 50 allocations
+                #println("E-max for this walker: ", E_max)
+                #println("Starting energy of this walker: (should be lower than E-max)", ase.eval_energy(NS.walkers[replace_walker],LJ,force_recalc = true))
+                walk_single_walker!(NS.walkers[replace_walker],LJ,NS.walker_params,E_max)
+                #return nothing            
+                #println("Ending energy of this walker: (should be lower than E-max)", ase.eval_energy(NS.walkers[replace_walker],LJ,force_recalc = true))
+    #            randomWalk!(NS.walkers[replace_walker],LJ,energyCutoff,NS.n_iter)
+            end
+            i += 1
+            V = ((NS.n_walkers - NS.n_cull + 1)/(NS.n_walkers + 1))^i
+            write(io,string(V) * " ")
+            write(io,string(E_max) * " \n")
         end
-        i += 1
-        V = ((NS.n_walkers - NS.n_cull + 1)/(NS.n_walkers + 1))^i
-        write(io,string(V) * " ")
-        write(io,string(E_max) * " \n")
-
+        println("Elapsed time for iteration $i: ", elapsed)
+        write(io,"$i $elapsed\n")
     end
-
     close(io)
 end
 
diff --git a/src/my_files/Figure_1.png b/src/my_files/Figure_1.png
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diff --git a/src/my_files/NS.out b/src/my_files/NS.out
new file mode 100644
index 0000000..60c527b
--- /dev/null
+++ b/src/my_files/NS.out
@@ -0,0 +1,1004 @@
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diff --git a/src/my_files/time.py b/src/my_files/time.py
new file mode 100644
index 0000000..83312db
--- /dev/null
+++ b/src/my_files/time.py
@@ -0,0 +1,21 @@
+import matplotlib.pyplot as plt
+
+with open(r'C:\Users\rexja\OneDrive - BYU-Idaho\Classes\Nelson Research Group\MatSim.jl\src\my_files\NS.out', 'r') as file:
+    lines = file.readlines()
+
+# Process the data
+x = []
+y = []
+for i, line in enumerate(lines):
+    if i % 2 == 1 and i > 4:
+        parts = line.split(" ")
+        if len(parts) == 2:
+            x.append(float(parts[0]))
+            y.append(float(parts[1]))
+
+# Plot the data
+plt.plot(x, y)
+plt.xlabel('Epoch')
+plt.ylabel('Wall time (s)')
+plt.title('NS Wall Time vs Epoch')
+plt.show()
\ No newline at end of file
diff --git a/src/scripts/NS-Rexs-Laptop.jl b/src/scripts/NS-Rexs-Laptop.jl
deleted file mode 100644
index 7603233..0000000
--- a/src/scripts/NS-Rexs-Laptop.jl
+++ /dev/null
@@ -1,73 +0,0 @@
-
-
-cDir = @__DIR__
-cd(cDir)
-push!(LOAD_PATH,joinpath(cDir,"../libraries"))
-#cd("C:\\Users\\rexja\\OneDrive - BYU-Idaho\\Classes\\Nelson Research Group\\MatSim.jl\\src\\libraries")
-push!(LOAD_PATH,pwd())
-
-using ase
-using LennardJones
-using nSampling
-using YAML
-
-# Initialize the model
-resultsPath = joinpath(cDir,"draws-LJ.Pt-Ag")
-
-# Build model with averages of the draws for fit parameters.
-LJ_average = LennardJones.get_LJ_averages(resultsPath)
-input = YAML.load_file(joinpath(cDir,"NS.yml"))
-myNS = nSampling.initialize(input["params"],LJ_average);# Initialize the simulation...
-nSampling.tune_step_sizes!(myNS,LJ_average)
-nSampling.run_NS(myNS,LJ_average)
-
-
-# Disregard all below
-# display(ase.eval_KE(myNS.walkers[sEnergies[end-3]]))
-# println(myNS.walkers[sEnergies[end-3]].coordSys)
-# myNS.walkers[4].lj_vec
-# ase.eval_forces(myNS.walkers[1],LJ_average)
-# display(ase.get_neighbor_distances(myNS.walkers[1],4.0))
-# println(myNS.walker_params.MD_time_step)
-# nSampling.tune_step_sizes(myNS.walkers[sEnergies[end-2]],myNS.walker_params,LJ_average,E_max)
-
-# ase.eval_KE(myNS.walkers[4])
-# sum(0.5 * [x' * x for x in myNS.walkers[4].velocities])
-# nSampling.run_NS(myNS,LJ_average)
-# check =ase.get_nn_list(myNS.walkers[2],5.6)
-# check = myNS.walkers[1].positions
-# myvec = ["ab", "dc", "ef"]
-# !("ab" in myvec)
-# println(myNS.walkers[1].lVecs)
-# println(ase.cell_volume(myNS.walkers[1]))
-# ase.DirectToCartesian!(myNS.walkers[1])
-# myNS.walker_params.MD_time_step = 0.000001
-# ase.do_MD!(myNS.walkers[3],LJ_average,myNS.walker_params,E_max)
-# 2 .* check #.* [2 * 5.0 ./ x for x in check] #.* 2 .* check
-# [2 * 5.0 ./ x for x in check] #.* 2 .* check
-# print(myNS.walkers[5].positions)
-# begin_energy = ase.eval_energy(myNS.walkers[2],LJ_average)
-# using Plots
-# using StaticArrays
-# using LinearAlgebra
-# nSampling.walk_single_walker!(myNS.walkers[2],LJ_average,myNS.walker_params,ase.eval_energy(myNS.walkers[2],LJ_average))
-# display(ase.eval_energy(myNS.walkers[2],LJ_average))
-# ase.gradientForce(LJ_average,myNS.walkers[2],@SVector[1,4],@SVector[2,2,2])
-# println(myNS.walkers[2].fitEnergy)
-# display(myNS.walkers[2].lVecs)
-# display(myNS.walkers[2].atomicBasis)
-# ase.mapIntoCell(myNS.walkers[2])
-# ase.DirectToCartesian!(myNS.walkers[2])
-
-# using LinearAlgebra
-# nHat = [[norm(x) > 0.0 ? x / norm(x) : x for x in y] for y in myNS.walkers[2].atomicBasis ]
-
-# any([isnan(z) for x in myNS.walkers[2].atomicBasis for y in x for z in y])
-# any(isnan.(myNS.walkers[2].atomicBasis[1]))
-# floor(-0.5)
-# rand(1:5)
-# #nSampling.GMC(myNS.configs[55],500,LJ_average)
-# nSampling.run_NS(myNS,LJ_average)
-# rands = nSampling.get_random_displacements([2,3])
-
-# println(rands[2])
\ No newline at end of file
diff --git a/src/scripts/NS-Rexs-Laptop.out b/src/scripts/NS-Rexs-Laptop.out
deleted file mode 100644
index ce3f7d7..0000000
--- a/src/scripts/NS-Rexs-Laptop.out
+++ /dev/null
@@ -1,104 +0,0 @@
-N_walkers = 20
-N_cull = 6
-N_steps_per_walker = 2000
-eps = 0.001
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diff --git a/src/scripts/NS.out b/src/scripts/NS.out
index fa2a3c5..635bd27 100644
--- a/src/scripts/NS.out
+++ b/src/scripts/NS.out
@@ -2,103 +2,203 @@ N_walkers = 20
 N_cull = 6
 N_steps_per_walker = 2000
 eps = 0.001
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diff --git a/src/scripts/NS.yml b/src/scripts/NS.yml
index 6f44adf..e589569 100644
--- a/src/scripts/NS.yml
+++ b/src/scripts/NS.yml
@@ -1,6 +1,6 @@
 
 params:
-  n_Atoms: [5, 3]
+  n_Atoms: [12, 20]
   min_atom_separation: 1.5
   n_walkers: 20 # Number of walkers in the pool.
   n_cull: 6  # Number of walkers to remove at each iteration.

From d236ced030fcc9e0e68cdf26ce105c3e0632e699 Mon Sep 17 00:00:00 2001
From: RexWight <rexjared86@gmail.com>
Date: Sat, 28 Jun 2025 21:10:06 -0600
Subject: [PATCH 4/4] Updated values and output yml

---
 src/libraries/nSampling.jl                    |   9 +-
 src/my_files/results/40-40 1atm-2atm/NS-1.out | 504 ++++++++++++++++++
 .../results/40-40 1atm-2atm/NS-10.out         | 504 ++++++++++++++++++
 src/my_files/results/40-40 1atm-2atm/NS-2.out | 504 ++++++++++++++++++
 src/my_files/results/40-40 1atm-2atm/NS-3.out | 504 ++++++++++++++++++
 src/my_files/results/40-40 1atm-2atm/NS-4.out | 504 ++++++++++++++++++
 src/my_files/results/40-40 1atm-2atm/NS-5.out | 504 ++++++++++++++++++
 src/my_files/results/40-40 1atm-2atm/NS-6.out | 504 ++++++++++++++++++
 src/my_files/results/40-40 1atm-2atm/NS-7.out | 504 ++++++++++++++++++
 src/my_files/results/40-40 1atm-2atm/NS-9.out | 504 ++++++++++++++++++
 src/my_files/results/40-40 1atm-2atm/NS.yml   |  25 +
 .../40-40 1atm-2atm/Pressure values.txt       |  13 +
 src/scripts/NS.jl                             |   2 +-
 src/scripts/NS.yml                            |   2 +-
 14 files changed, 4580 insertions(+), 7 deletions(-)
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS-1.out
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS-10.out
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS-2.out
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS-3.out
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS-4.out
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS-5.out
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS-6.out
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS-7.out
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS-9.out
 create mode 100644 src/my_files/results/40-40 1atm-2atm/NS.yml
 create mode 100644 src/my_files/results/40-40 1atm-2atm/Pressure values.txt

diff --git a/src/libraries/nSampling.jl b/src/libraries/nSampling.jl
index a8ec432..8a13e87 100755
--- a/src/libraries/nSampling.jl
+++ b/src/libraries/nSampling.jl
@@ -225,21 +225,20 @@ function reverse_sort_energies(NS)
 
 end
 
-function run_NS(NS::NS,LJ::LennardJones.model)
+function run_NS(NS::NS,LJ::LennardJones.model, output_file)
     println("Reading the file")
     V = (NS.n_walkers - NS.n_cull + 1)/(NS.n_walkers + 1)
     cDir = pwd()
 
     i = 1
-    io = open(joinpath(cDir,"NS.out"),"w")
+    io = open(joinpath(cDir, output_file),"w")
     write(io, "N_walkers = " * string(NS.n_walkers) * "\n")
     write(io, "N_cull = " * string(NS.n_cull) * "\n")
     write(io, "N_steps_per_walker = " * string(NS.n_iter) * "\n")
     write(io, "eps = " * string(NS.eps) * "\n")
     perms = zeros(MVector{length(NS.walkers),Int})
 #    while V > NS.eps
-    for i= 1:500
-        elapsed = @elapsed begin 
+    for i= 1:5
             println(i)
             println("V = ", V)
             ## Find the top Kr highest energies
@@ -282,7 +281,7 @@ function run_NS(NS::NS,LJ::LennardJones.model)
         V = ((NS.n_walkers - NS.n_cull + 1)/(NS.n_walkers + 1))^i
         write(io,string(V) * " ")
         write(io,string(E_max) * " \n")
-
+        
     end
     close(io)
 end
diff --git a/src/my_files/results/40-40 1atm-2atm/NS-1.out b/src/my_files/results/40-40 1atm-2atm/NS-1.out
new file mode 100644
index 0000000..745e743
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS-1.out	
@@ -0,0 +1,504 @@
+N_walkers = 200
+N_cull = 1
+N_steps_per_walker = 2000
+eps = 1.0e-8
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diff --git a/src/my_files/results/40-40 1atm-2atm/NS-10.out b/src/my_files/results/40-40 1atm-2atm/NS-10.out
new file mode 100644
index 0000000..1a907c1
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS-10.out	
@@ -0,0 +1,504 @@
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diff --git a/src/my_files/results/40-40 1atm-2atm/NS-2.out b/src/my_files/results/40-40 1atm-2atm/NS-2.out
new file mode 100644
index 0000000..7a93d9d
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS-2.out	
@@ -0,0 +1,504 @@
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diff --git a/src/my_files/results/40-40 1atm-2atm/NS-3.out b/src/my_files/results/40-40 1atm-2atm/NS-3.out
new file mode 100644
index 0000000..a778902
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS-3.out	
@@ -0,0 +1,504 @@
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diff --git a/src/my_files/results/40-40 1atm-2atm/NS-4.out b/src/my_files/results/40-40 1atm-2atm/NS-4.out
new file mode 100644
index 0000000..d7aeb18
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS-4.out	
@@ -0,0 +1,504 @@
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diff --git a/src/my_files/results/40-40 1atm-2atm/NS-5.out b/src/my_files/results/40-40 1atm-2atm/NS-5.out
new file mode 100644
index 0000000..6bf0d67
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS-5.out	
@@ -0,0 +1,504 @@
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diff --git a/src/my_files/results/40-40 1atm-2atm/NS-6.out b/src/my_files/results/40-40 1atm-2atm/NS-6.out
new file mode 100644
index 0000000..4099f9c
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS-6.out	
@@ -0,0 +1,504 @@
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diff --git a/src/my_files/results/40-40 1atm-2atm/NS-7.out b/src/my_files/results/40-40 1atm-2atm/NS-7.out
new file mode 100644
index 0000000..e9b0ba9
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS-7.out	
@@ -0,0 +1,504 @@
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diff --git a/src/my_files/results/40-40 1atm-2atm/NS-9.out b/src/my_files/results/40-40 1atm-2atm/NS-9.out
new file mode 100644
index 0000000..62aa7e3
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS-9.out	
@@ -0,0 +1,504 @@
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diff --git a/src/my_files/results/40-40 1atm-2atm/NS.yml b/src/my_files/results/40-40 1atm-2atm/NS.yml
new file mode 100644
index 0000000..ae1c31e
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/NS.yml	
@@ -0,0 +1,25 @@
+
+params:
+  n_Atoms: [40, 40]
+  min_atom_separation: 1.5
+  n_walkers: 200 # Number of walkers in the pool.
+  n_cull: 1  # Number of walkers to remove at each iteration.
+  atom_traj_length: 8 # Length of random walk.
+  eps: 1e-8 # Algorithm stopping criteria
+  n_iter: 2000  # Number of NS iterations per walker.
+  atom_algorithm: MD # GMC,MC, MD 
+  MC_atom_step_size: 0.0005  # Displacements of atoms in GMC as a multiple of max length between atoms (max_vol_per_atom * n_atoms)^(1/3))
+  MD_time_step: 5.0e-5
+  MD_reject_eps: 1e-4  # If the energy during MD trajectory changes by more than <MD_reject_eps> * KE_max, we reject it.  
+  n_single_walker_steps: 500  # Number of steps that a single walker should take (long enough to decorrelate)  
+  n_atom_steps: 10
+  n_cell_volume_steps: 5
+  n_cell_shear_steps: 8
+  n_cell_stretch_steps: 8
+  cell_P: 1.20e-6 # Atmospheric Pressure in units of eVs / A^3
+  min_aspect_ratio: 0.8
+  max_volume_per_atom: 64.0
+  volume_step_size: 0.5  # Actually volume per atom step size.
+  shear_step_size: 0.2
+  stretch_step_size: 0.1
+output: "NS-out/NS-10.out"
diff --git a/src/my_files/results/40-40 1atm-2atm/Pressure values.txt b/src/my_files/results/40-40 1atm-2atm/Pressure values.txt
new file mode 100644
index 0000000..e6f6bf5
--- /dev/null
+++ b/src/my_files/results/40-40 1atm-2atm/Pressure values.txt	
@@ -0,0 +1,13 @@
+Pressues in ev/ų
+
+1 6.32E-07 
+2 6.96E-07
+3 7.59E-07
+4 8.22E-07
+5 8.85E-07
+6 9.48E-07
+7 1.01E-06
+8 1.07E-06
+9 1.14E-06
+10 1.20E-06
+
diff --git a/src/scripts/NS.jl b/src/scripts/NS.jl
index e47014f..973531d 100644
--- a/src/scripts/NS.jl
+++ b/src/scripts/NS.jl
@@ -15,5 +15,5 @@ input = YAML.load_file(joinpath(cDir,"NS.yml"))
 LJ_average = LennardJones.get_LJ_averages(resultsPath)
 myNS = nSampling.initialize(input["params"],LJ_average);# 10k allocations.  Need to optimize this.
 nSampling.tune_step_sizes!(myNS,LJ_average)
-nSampling.run_NS(myNS,LJ_average)
+nSampling.run_NS(myNS,LJ_average, input["output"])
 
diff --git a/src/scripts/NS.yml b/src/scripts/NS.yml
index 327f84e..01efa91 100644
--- a/src/scripts/NS.yml
+++ b/src/scripts/NS.yml
@@ -22,4 +22,4 @@ params:
   volume_step_size: 0.5  # Actually volume per atom step size.
   shear_step_size: 0.2
   stretch_step_size: 0.1
-
+output: "NS1.out"