Intro.md

Intro

About Snakefile

The Snakefile sets up a series of rules for calculation. It decomposes the workflow into small steps. We only need to specify the filename of final output, and the Snakefile will figure out the rule which outputs this filename. And it will look for the inputs of this rule. If there is no input available in the directory, but are rules that can generate these inputs. It will automatically run these rules to make inputs first. The rules in Snakefile are written in order.

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We will step through a VMC calculation for molecule H₂ with bond length r=1.4 and basis ccpvtz.

Generate Geometry

First we need to initiate the file {dir}/geom.xyz.

{dir}=h2_1.4/hf/vtz

We used to name directories in this way, so we can use gather.py later to deal with data.

And geom.xyz should contain

H 0. 0. 0.
H 0. 0. 1.4

We choose the starting wavefunction for VMC to be generated by Restricted Hartree-Fork using pyscf in rule MEAN_FIELD. If we want the starting wavefunction from Unrestricted Hartree-Fork, we should name {dir}=h2_1.4/uhf/vtz.

Optimization

The rule OPTIMIZE_MF and rule OPTIMIZE_HCI optimize the starting wavefunction for VMC.

For rule OPTIMIZE_MF, we need to specify variables for the output.

{variables}={startingwf}_{orbitals}_{statenumber}_{nconfig}

rule VMC will take the same variables.

Rule VMC

rule VMC:
    input: mf = "{dir}/mf.chk", opt = "{dir}/opt_{variables}.chk"
    output: "{dir}/vmc_{variables}.chk"
    run: 
        #calculations#

In the calculations it will call functions in functons.py, which import functions from pyscf and pyqmc.

As talked before, rule VMC will automatically look for the inputs. Therefore, it will run

• rule DEFAULT_SETTINGS
• rule MEAN_FIELD
• rule OPTIMIZE_MF

in order before rule VMC.

Run VMC

We can run the following command

snakemake.snakemake("Snakefile",cores=1,targets=["h2_1.4/hf/vtz/vmc_mf_orbitals_0_400.chk"])

In run_workflow.py, we generate a list of filenames. We only need to call Snakemake once, by replacing with targets=[list of filenames].

Other calculations

We also have rule CC, rule HCI, rule DMC, etc. The calculations will be done similar to VMC.

Gather data

The gather.py will gather and calculate data such as energy and entropy from the outputs(.chk files) and generate a csv file. See more details in shunyue's or Nirvaan's branch.