Python

Python

CrySPY 1.1.0 or later

• Python >= 3.8
  • PyXtal (>= 0.5.3)
  • (optional) mpi4py
  • (optional, required if algo is BO) COMBO

If you install cryspy with pip, necessary libraries such as PyXtal will be installed automatically. Go to Installation > CrySPY. Manual installation of COMBO is required when using Bayesian optimization.

CrySPY 1.0.0

• Python >= 3.8
  • PyXtal (>= 0.5.3)
  • (optional, required if algo is BO) COMBO

CrySPY 0.10.0 – 0.10.3

Tested with Homebrew Python 3.8.x and 3.9.x on Mac and Python 3.8.x on Linux.

• Python 3.x.x
  • COMBO
  • PyXtal (>= 0.2.2)
  • (PyXtal requires pymatgen) pymatgen (>= 2022.x.x)

CrySPY 0.9.2

Tested with Homebrew Python 3.8.x and 3.9.x on Mac and Python 3.8.x on Linux.

• Python 3.x.x
  • COMBO
  • pymatgen (>= 2022.x.x)
  • PyXtal (>= 0.2.2)

CrySPY 0.9.0 – 0.9.1

• Python 3.8.x
  • COMBO
  • pymatgen (<= 2021.x.x)
  • PyXtal 0.1.6 - 0.2.1

CrySPY 0.8.0 or earlier

See the old document which is included CrySPY itself.

Structure optimizer

Structure optimizer

At least one optimizer is required.

• First-principles calculation
  • VASP
  • QUANTUM ESPRESSO
  • OpenMX (CrySPY 0.9.0 or later)
• Interatomic potential
  • soiap
  • LAMMPS
• Other
  • ASE (CrySPY 1.2.0 or later)

find_wy (optional)

CrySPY have utilized find_wy to generate a random structure for a given space group (symmetry). However, CrySPY employs PyXtal library for structure generation as default since version 0.9.0. You can skip to install find_wy in CrySPY 0.9.0 or later, but you may use find_wy. For CrySPY 0.8.x or earlier, find_wy is required to generate a random structure for a given space group.

Installation of find_wy

m_tspace

First you need compile m_tspace for find_wy. Check these sites to compile it.

• m_tspace
• Wiki of m_tspace

Download the source code of m_tspace in an arbitrary directory. For example:

$ mkdir -p ~/local
$ cd ~/local
$ git clone https://github.com/nim-hrkn/m_tspace.git

Additional two files are required to compile m_tspace. Download the following files in ~/local/m_tspace from TSPASE:

• tsp98.f
• prmtsp.f

$ cd m_tspace
$ wget http://phoenix.mp.es.osaka-u.ac.jp/~tspace/tspace_main/tsp07/tsp98.f
$ wget http://phoenix.mp.es.osaka-u.ac.jp/~tspace/tspace_main/tsp07/prmtsp.f

Edit the makefile and run the make command. If you use ifort, you had better delete -check all option and use -O2 option.

$ emacs makefile
$ head -n 4 makefile
#FC=gfortran
#FFLAGS=-g -cpp -DUSE_GEN -ffixed-line-length-255
FC=ifort
FFLAGS=-O2 -g -traceback -cpp -DUSE_GEN -132
$ make

If you used gfortran, you might face the following problem:

tsp98.f:9839:32:

       CALL SUBGRP(MG,JG,MGT,JGT,NTAB,IND)
                                1
Error: Actual argument contains too few elements for dummy argument 'ntab' (12/48) at (1)
make: *** [tsp98.o] Error 1

Then change the source file of tsp98.f like this (line 9925):

Before:

9913: C SUBROUTINE SUBGRP ====*====3====*====4====*====5====*====6====*====7
9914: C
9915: C    IF (JG(I),I=1,MG) IS A SUBGROUP OF (JGT(J),J=1,MGT) THEN
9916: C          TABLE (NTAB(I),I=1,MG) IS MADE HERE AND IND=0
9917: C    ELSE
9918: C          IND=-1
9919: C
9920: C                 1993/12/25
9921: C                   BY  S.TANAKA AND A. YANASE
9922: C---*----1----*----2----*----3----*----4----*----5----*----6----*----7
9923: C
9924:       SUBROUTINE SUBGRP(MG,JG,MGT,JGT,NTAB,IND)
9925:       DIMENSION NTAB(48),JG(48),JGT(48)

After:

9913: C SUBROUTINE SUBGRP ====*====3====*====4====*====5====*====6====*====7
9914: C
9915: C    IF (JG(I),I=1,MG) IS A SUBGROUP OF (JGT(J),J=1,MGT) THEN
9916: C          TABLE (NTAB(I),I=1,MG) IS MADE HERE AND IND=0
9917: C    ELSE
9918: C          IND=-1
9919: C
9920: C                 1993/12/25
9921: C                   BY  S.TANAKA AND A. YANASE
9922: C---*----1----*----2----*----3----*----4----*----5----*----6----*----7
9923: C
9924:       SUBROUTINE SUBGRP(MG,JG,MGT,JGT,NTAB,IND)
9925:       DIMENSION NTAB(12),JG(48),JGT(48)

If you succeed in compiling, you get m_tsp.a.

find_wy

Check these sites to compile find_wy:

• find_wy
• Wiki of find_wy

Download the source code of find_wy in an arbitrary directory. For example:

$ mkdir -p ~/local
$ cd ~/local
$ git clone https://github.com/nim-hrkn/find_wy.git

Edit make.inc and set the path to the m_tsp.a that you just prepared.

$ cd find_wy
$ emacs make.inc
$ head -n 4 make.inc
TSPPATH=~/local/m_tspace
#INCPATH = -I $(TSPPATH)
TSP=$(TSPPATH)/m_tsp.a

You can delete -check all option and use -O2 option. Then run the make command.

$ make

When you get the executable file of find_wy, run the following command for test:

$ ./find_wy input_sample/input_si4o8.txt

If there is no problem, POS_WY_SKEL_ALL.json file is generated.

Executable file of find_wy

CrySPY 1.0.0 or later

Put the executable file of find_wy in your PATH. Or, specify the path of the executable file in cryspy.in as follows:

[structure]
use_find_wy = True
fwpath = /xxx/xxx/xxx/find_wy

CrySPY 0.10.3 or earlier

When you use find_wy, put the executable file of find_wy in ~/CrySPY_root/CrySPY-x.x.x/CrySPY/find_wy/, so that the executable file path is ~/CrySPY_root/CrySPY-x.x.x/CrySPY/find_wy/find_wy.