mcgridprep

Helper tool to easily run 2D grids for H2O using OpenMolcas.

Installation

cd [where you wan't to install it]
git clone https://github.com/eljost/mcgridprep
cd mcgridparse
python setup.py develop

Overview

mcgridprep provides four commands:

mcgridprep # Prepares all input files
mcgridrun [job_inputs] [--cpus N] # Runs OpenMolcas with the generated inputs
mcgridparse # Parses all data from the log files and/or HDF5 files
mcgridplot # Plots the parsed data (PES, polarizabilities, ...)

Configuration

mcgridprep reads the grid configuration from a .yaml file called mcgrid.yaml.

# Optional.  Will be used to name the files generated by mcgridprep
#name: wasser_grid
charge: 0
spin: 1
# Supported methods are: [hf, mp2, cas, caspt2, loprop]
# If loprop is set it will be called with the method before it
methods: [cas, caspt2]
basis: aug-cc-pvtz
# If using method cas this should be set to an INPORB file with the appropriate basis.
# Ideally this file was created by a &rasscf calculation at the starting point coord_eq.
inporb: /scratch/molcas_jobs/water_rigid/backup/07_rasscf_augtz/water_rigid.RasOrb
# Optional. Set this if you want to include excited states.
#ciroot: 2
# Path were the RasOrb/JobIph/moldens/h5 files are saved. Can be left at it's default value.
backup_path: backup
# Specification of 2D grid axes. They are given as [start, end, step].
coord1: [110, 90, 5]
coord2: [0.7, 1.1, 0.1]
# Axes labels for the plots. Can be left at their default values if coord1 is the angle
# and coord2 is the symmetric stretch.
coord1_lbl: "∠(H-O-H) / deg"
coord2_lbl: "r(O-H)_sym / Å"
# The starting point of the grid. Ideally this  point lies on the grid and corresponds
# to the equilibrium geometry. The inporb fil specified above should have been generated
# at this geometry.
coord_eq: [101, 1.0]

To be able to run mcgridrun all appropriate variables for OpenMolcas have to be set! This usually involves sourcing a little shell scrip with the appropriate environment variables before running mcgridrun. An example is provided below.

#!/bin/bash

# Load all appropriate libraries/modules here

export MOLCAS_NPROCS=1
export MOLCAS_PRINT=2
export MOLCAS_MEM=4000
export MOLCAS_MOLDEN=ON
export MOLCAS_OUTPUT=$CurrDir
export OMP_NUM_THREADS=1
# This should be adapted to your installation
export MOLCAS=/scratch/programme/openmolcas_serial

So before you run mcgridrun just source the above bash script with source setmolcas.sh. This assumes you saved the shellscript as setmolcas.sh.

Running calculations

To setup a calculation you just have to decide on the two grid coordinates (coord1, coord2), select an appropriate starting point (coord_eq) and prepare an INPORB (inporb) file if you want to use the &rasscf module. A template for the mcgrid.yaml file can be found in the mcgridprep subfolder of the git repository (mcgrid.yaml template).

Basic steps

Create a folder and prepare mcgrid.yaml in it. This folder will be called [root].
Run mcgridprep in [root]. This creates all OpenMolcas inputs and a file called job_inputs containing a list of all generated inputs.
Excecute mcgridrun job_inputs --cpus 4 to run all jobs stored in job_inputs with four calculations in parallel. --cpus should be set to an appropriate number.
After or while the calculations are running you can call mcgridparse to extract the calculated informations. The command should be run from the [root] folder.
To plot the data run mcgridplot in [root].

Working example

A working example can be found in the tests/01_example subfolder. You just have to adapt the inporb path in mcgrid.yaml and the MOLCAS variable in setmolcas.sh. To run everything:

cd tests/01_example
mcgridprep
source setmolcas.sh
mcgridrun job_inputs --cpus 4
mcgridparse
mcgridplot