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nexus script to generate pyscf input with twists
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Kevin Gasperich
parent
1277f78d72
commit
1efe61efd0
244
src/utils_complex/generate_pyscf_twists.py
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244
src/utils_complex/generate_pyscf_twists.py
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#! /usr/bin/env python
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from nexus import settings,job,run_project,obj
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from nexus import generate_physical_system
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from nexus import generate_pyscf
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import spglib
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import numpy as np
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import os
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settings(
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results = '',
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sleep = 3,
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machine = 'ws8',
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generate_only=1,
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)
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solid_tmp_file = './.tmp_solid_template.py'
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jobparams={}
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jobparams['dfname'] = 'df_ints.h5'
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jobparams['chkname'] = 'diamond.chk'
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jobparams['dftype'] = 'GDF'
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jobparams['auxbasis'] = 'weigend'
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jobparams['xc'] = 'b3lyp'
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show_kmap = True
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pyscf_job = job(cores=1,serial=True)
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cell_types = [
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'diamond_8_real',
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# 'diamond_8_comp',
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]
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cell_info = obj(
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diamond_8_real = obj(
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# tiling = [[ 1, -1, 1],
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# [ 1, 1, -1],
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# [-1, 1, 1]],
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tiling = (2,2,2),
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kgrid = (6,6,6),
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),
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)
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a = 3.37316115
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axes = np.array([[a,a,0],[0,a,a],[a,0,a]])
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elem = ['C','C']
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pos = [[0,0,0],[a/2,a/2,a/2]]
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scf_info = obj(
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basis = 'bfd-vdz',
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ecp = 'bfd',
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drop_exponent = 0.1,
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verbose = 5,
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)
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tempstr = """
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#!/usr/bin/env python
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'''
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Gamma point post-HF calculation needs only real integrals.
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Methods implemented in finite-size system can be directly used here without
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any modification.
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'''
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import numpy as np
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from pyscf import lib
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from pyscf.pbc import gto, scf, dft
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from pyscf import gto as Mgto
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from pyscf.pbc import df
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from pyscf.pbc import ao2mo
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from pyscf.pbc import tools
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from pyscf.pbc.tools.pbc import super_cell
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from functools import reduce
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import scipy.linalg as la
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import os
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restart = False
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$system
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$twistinfo
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pwd_top = os.path.dirname(os.path.realpath(__file__))
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for i in range(2,3):
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jobdir=pwd_top + '/twist-{:02d}/'.format(i)
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if not restart:
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os.mkdir(jobdir)
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os.chdir(jobdir)
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sp_twist=supTwist[i]
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kpts_i=allkpts[i]
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print("i ",i, kpts_i)
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supcell=cell
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mydf = df.$dftype(supcell,kpts_i)
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mydf.auxbasis = '$auxbasis'
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dfpath = jobdir+'$dfname'
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if not restart:
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mydf._cderi_to_save = dfpath # new
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mydf.build() # new
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#end if
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mf = scf.KROKS(supcell,kpts_i).density_fit()
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mf.xc='$xc'
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mf.tol = 1e-10
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mf.exxdiv = 'ewald'
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mf.with_df = mydf
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chkpath = jobdir + '$chkname'
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mf.chkfile = chkpath
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mf.with_df._cderi = dfpath
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if restart:
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dm = mf.from_chk(chkpath) # restart
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e_scf=mf.kernel(dm) # restart
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else:
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e_scf=mf.kernel() # new
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#end if
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with open('e_scf','w') as ener:
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ener.write('%s\n' % (e_scf))
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print('e_scf',e_scf)
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#title="S8-twist%s"%i
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#### generated conversion text ###
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#from PyscfToQmcpack import savetoqmcpack
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#savetoqmcpack(cell,mf,title=title,kmesh=kmesh,kpts=kpts_i,sp_twist=sp_twist)
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mycas = list(range(0,30))
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#title="S8-Cas30-twist%s"%i
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#### generated conversion text ###
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#from PyscfToQmcpack import savetoqmcpack
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#savetoqmcpack(cell,mf,title=title,kmesh=kmesh,kpts=kpts_i,sp_twist=sp_twist, cas_idx=mycas)
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#### end generated conversion text ###
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from MolPyscfToQPkpts import pyscf2QP2
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pyscf2QP2(supcell,mf,kpts=kpts_i,int_threshold = 1E-15,cas_idx=mycas)
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print('Done for Tw%s'%i)
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os.chdir(pwd_top)
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"""
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#replace $dfname with df_ints.h5
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#replace $chkname with checkpoint file name
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#$dftype is GDF, MDF, etc.
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#$auxbasis weigend?
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#$xc b3lyp
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#$twistinfo
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for cell_type in cell_types:
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cell_tiling = cell_info[cell_type].tiling
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cell_kgrid = cell_info[cell_type].kgrid
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diamond = generate_physical_system(
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# axes = '''
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# 3.37316115 3.37316115 0.00000000
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# 0.00000000 3.37316115 3.37316115
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# 3.37316115 0.00000000 3.37316115''',
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# elem_pos = '''
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# C 0.00000000 0.00000000 0.00000000
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# C 1.686580575 1.686580575 1.686580575''',
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axes = axes,
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elem = elem,
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pos = pos,
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units = 'B',
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tiling = cell_tiling,
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kgrid = cell_kgrid,
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kshift = (0,0,0),
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C = 4,
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symm_kgrid=True,
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)
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jobparams['twistinfo'] = ''
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if show_kmap:
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print (cell_type)
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print ('===============================')
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s = diamond.structure.copy()
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kmap = s.kmap()
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print ('supercell kpoints/twists')
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jobparams['twistinfo']+='# supercell kpoints/twists\n'
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jobparams['twistinfo']+='supTwist=array([\n'
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for i,k in enumerate(s.kpoints):
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print (' ',i,k)
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jobparams['twistinfo']+=(str(list(k))+',\n')
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#end for
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jobparams['twistinfo']+='])\n'
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print ('primitive cell kpoints')
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# this should already be written by nexus as part of $system
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#jobparams['twistinfo']+='# primitive cell kpoints\n')
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#jobparams['twistinfo']+='orig=array([\n'
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for i,k in enumerate(s.folded_structure.kpoints):
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print (' ',i,k)
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#jobparams['twistinfo']+=(str(list(k))+',\n')
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#end for
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#jobparams['twistinfo']+='])\n'
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jobparams['twistinfo']+='# mapping from supercell to primitive cell k-points\n'
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jobparams['twistinfo']+='mymap=array([\n'
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for kmapkey in kmap.sorted_keys():
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jobparams['twistinfo']+=(str(list(kmap[kmapkey]))+',\n')
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jobparams['twistinfo']+='])\n'
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print ('mapping from supercell to primitive cell k-points')
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print (kmap)
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#jobparams['twistinfo']+=('allkpts=array(list(map(lambda xs: list(map(lambda x: orig[x], xs)), mymap)))\n')
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jobparams['twistinfo']+=('allkpts=array(list(map(lambda xs: list(map(lambda x: kpts[x], xs)), mymap)))\n')
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jobparams['twistinfo']+=('kweights=array('+str(list(s.kweights))+')\n')
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#end if
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tmp_template = tempstr
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for key in jobparams.keys():
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tmp_template = tmp_template.replace('$'+key,jobparams[key])
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if os.path.isfile(solid_tmp_file):
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raise Exception(solid_tmp_file,'solid_tmp_file already exists: delete file and try again')
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with open(solid_tmp_file,'w') as stmp:
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stmp.write(tmp_template)
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scf = generate_pyscf(
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identifier = 'scf',
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path = cell_type,
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job = pyscf_job,
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template = solid_tmp_file,
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system = diamond,
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cell = scf_info,
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# cell = obj(
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# basis = 'bfd-vtz',
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# ecp = 'bfd',
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# drop_exponent = 0.1,
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# verbose = 5,
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# ),
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save_qmc = True ,
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)
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if os.path.isfile(solid_tmp_file):
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os.remove(solid_tmp_file)
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#end for
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#if show_kmap:
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# exit()
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#end if
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run_project()
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