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Calypso Workflow

1. Pseudopotential Preparation (Consistent with VASP)

Obtain pseudopotential folder PsePot (generally use pbe)

Usage: cat POTCAR_1 POTCAR_2 …… POTCAR_n >> POTCAR

Note: The order when combining potcar must be consistent with input.dat

2. Prepare Files

Files to copy:

From the example folder in the Calypso installation path, copy the following files:

(1) input.dat

(2) INCAR_* (i.e., all INCAR files, used for VASP multiple optimizations from low to high precision, total of four)

(3) The just-combined POTCAR file (Note: name must be POTCAR only, otherwise not recognized)

(4) Submission script (vasp.pbs)

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#!/bin/bash
#PBS -N calypso
#PBS -l nodes=1:ppn=12
#PBS -j n
#PBS -e ${PBS_JOBNAME}.err
#PBS -o ${PBS_JOBNAME}.out
cd $PBS_O_WORKDIR
NP=`cat $PBS_NODEFILE|wc -l` #Modify above section according to specific server
/share/apps/Calypso/calypso5.0/calypso_dev/Src/calypso.x > log2 2>&1
#Modify according to specific executable file path

And script submit.sh:

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#!/bin/sh
mpirun -n 12 /share/apps/VASP/V5.3.2/vasp5.3.2.std.impi > log1 2>/dev/null

Modify path section to specific path

3. Edit Files

(1) input.dat

Basics are in Calypso Chinese Manual Chapter 2

First few items related to compound chemical formula must be changed

Search volume by pressure on this website, or add two atomic volumes and divide by 2: https://uspex-team.org/online_utilities/volume_estimation/

Interatomic distances:

Find the RCORE field in the POTCAR of each element composing the searched compound, multiply its value by 0.529 then multiply by 0.6~0.8 to get the estimated value, then add them

Order is: * A-A A-B * B-A B-B (A-B=B-A)

Popsize and Maxstep together determine search structure efficiency. Setting them higher reduces efficiency but makes results more accurate. Can be adjusted according to specific needs.

Variable composition prediction: (This part can be deleted for fixed composition)

If this parameter doesn't exist, add:

MaxNumAtom=integer: In variable composition structure prediction, the maximum number of atoms allowed to predict in the simulation cell. Default value: 20

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@CtrlRange
integer11 integer12   e.g. 1 3
integer21 integer22        1 3
@End

Defines the range of atomic number variation for each element in a binary system. For A atoms, x ranges from integer11 to integer12, and for B atoms, y ranges from integer21 to integer22. Default values: 1 6 1 6

If parameters are added here, they will override the previous NumberofAtoms parameter, making it ineffective.

(2) INCAR files, all 4 need to be changed

System local optimization

Modify the value below Target Pressure, unit is kbar, 1GPa = 10kbar. For example, for 100GPa, modify the value to 1000

4. Submit, View and Delete Tasks

Supercomputing Center: * Submit: bsub < u.lsf * View: bjobs * Delete: bkill task_name

Physics Department: * Submit: qsub script_name * View: qstat * Delete: qdel task_name

5. Results Analysis

In results folder

  • cak.py Generate results analysis file with .dat suffix
  • cak.py -m accuracy --vasp Output VASP format file
  • cak.py --cif Output cif image file

Notes: If it finishes running quickly and generates a series of pso_sor, ini, opt files, but the analysis file is all NULL, check whether VASP was not correctly called. Generally, modifying the VASP executable file path will fix this.