/usr/share/psi/python/mbe_impl.py is in psi4-data 1:0.3-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 | # #
# #@BEGIN LICENSE
# #
# # PSI4: an ab initio quantum chemistry software package
# #
# # This program is free software; you can redistribute it and/or modify
# # it under the terms of the GNU General Public License as published by
# # the Free Software Foundation; either version 2 of the License, or
# # (at your option) any later version.
# #
# # This program is distributed in the hope that it will be useful,
# # but WITHOUT ANY WARRANTY; without even the implied warranty of
# # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# # GNU General Public License for more details.
# #
# # You should have received a copy of the GNU General Public License along
# # with this program; if not, write to the Free Software Foundation, Inc.,
# # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
# #
# #@END LICENSE
# #
# #from parallel import *
# #from qmmm import *
# #import sys
#
# #Our instance of the MBE c++ API
# lfrag=psi4.LibFragHelper()
#
# def Done():
# global lfrag
# del lfrag
#
# def MakePointChargeEmbed(N,frag):
# charges=lfrag.EmbedHelper(N,frag)
# qmmm=QMMM()
# for i in range(0,len(charges)/4):
# qmmm.addChargeBohr(charges[i*4],charges[i*4+1],charges[i*4+2],charges[i*4+3])
# if(len(charges)>=4):
# qmmm.populateExtern()
# psi4.set_global_option_python('EXTERN',qmmm.extern)
# return (len(charges)>=4)
#
# def NewMolecule(N,frag,molecule):
# atoms=lfrag.GetNMerN(N,frag)
# caps=lfrag.CapHelper(N,frag)
# ghosts=lfrag.GetGhostsNMerN(N,frag)
# old_geom=molecule.save_string_xyz()
# temp_geom=old_geom.split('\n')
# new_geom=[]
# for i in range(0,len(atoms)):
# new_geom.append(temp_geom[atoms[i]+1])
# new_geom.append(caps)
# for i in range(0,len(ghosts)):
# new_geom.append('@'+temp_geom[ghosts[i]+1].lstrip(' '))
# new_geom.append('symmetry c1')
# new_geom.append('no_reorient')
# new_geom.append('no_com')
# fragstr='\n'.join(new_geom)
# return geometry(fragstr)
#
# def GetOptions():
# DaOptions={}
# DaOptions['DF_BASIS_SCF']=psi4.get_global_option('DF_BASIS_SCF')
# DaOptions['DF_BASIS_MP2']=psi4.get_global_option('DF_BASIS_MP2')
# DaOptions['DF_BASIS_CC']=psi4.get_global_option('DF_BASIS_CC')
# return DaOptions
#
# def UpdateOptions(DaOptions):
# for k,v in DaOptions.iteritems():
# if(not ((DaOptions[k] == '') or (DaOptions[k] == 'NONE'))):
# psi4.set_global_option(k,DaOptions[k])
#
# def RunCalc(frag,name,molecule,Egys,CEgys,N,**kwargs):
# OldOptions=GetOptions()
# oldguess=psi4.get_global_option("GUESS")
# if(lfrag.WriteMOs(N,frag)==1):
# psi4.set_global_option("GUESS","READ")
# AreEmbedding=MakePointChargeEmbed(N,frag)
# frag=NewMolecule(N,frag,molecule)
# activate(frag)
# frag.update_geometry()
# UpdateOptions(OldOptions)
# Egys.append(energy(name,**kwargs))
# for k,v in CEgys.iteritems():
# CEgys[k].append(psi4.get_variable(k))
# if(AreEmbedding):
# psi4.set_global_option_python("EXTERN", None)
# oep=psi4.OEProp()
# oep.add("MULLIKEN_CHARGES")
# oep.compute()
# activate(molecule)
# molecule.update_geometry()
# if(N==0):
# lfrag.GatherData()
# psi4.set_global_option("GUESS",oldguess)
# psi4.clean()
#
# #Both the fragments and NMers go through the same sequence of calls,
# #we term them the basecall
#
# def BaseCall(name,molecule,Egys,CEgys,NStart,NEnd,SuppressPrint,itr,**kwargs):
# if(SuppressPrint):
# psi4.be_quiet()
# PMan=Parallel()
# sizes=[]
# for N in range(NStart,NEnd):
# sizes.append(lfrag.GetNNMers(N))
# for frag in range(0,sizes[N-NStart]):
# PMan.AddTask(str(N)+' '+str(frag),N)
# PMan.MakeJob()
# task=PMan.Begin()
# tempEgys=[]
# tempCEgys={}
# tempCEgys.fromkeys(CEgys.keys(),[])
# while(not PMan.Done()):
# frag=int(task.split(' ')[1])
# order=int(task.split(' ')[0])
# RunCalc(frag,name,molecule,tempEgys,tempCEgys,order,**kwargs)
# task=PMan.Next()
# R1=PMan.Synch(tempEgys,1)
# R2={}
# R2.fromkeys(CEgys.keys(),[])
# for k,v in tempCEgys.iteritems():
# R2[k]=PMan.Synch(tempCEgys[k],1)
# total=0
# for N in range(NStart,NEnd):
# offset=sizes[N-NStart]
# lfrag.Sync("COMM_WORLD",N,itr)
# Egys[N]=R1[total:total+offset]
# for k,v in tempCEgys.iteritems():
# CEgys[k][N]=R2[k][total:total+offset]
# total+=offset
# del PMan
# if(SuppressPrint):
# psi4.reopen_outfile()
#
# def setup(frag_method,N,embed_method,cap_method,bsse_method,IsSymm):
# lcfrag_method=frag_method.lower()
# lcbsse_method=bsse_method.lower()
# lcembed_method=embed_method.lower()
# lccap_method=cap_method.lower()
# Driver=psi4.LibFragDriver()
#
# lfrag.FragHelper(lcfrag_method,N,lcembed_method,lccap_method,
# lcbsse_method,IsSymm)
#
# def fragment(name,molecule,Egys,CEgys,SuppressPrint,**kwargs):
# if(lfrag.RunFrags()!=0):
# itr=0;
# done =False
# while (not done):
# if(itr>=1):
# #Reset energies
# del Egys[0][:]
# for k,v in CEgys.iteritems():
# del CEgys[v][0][:]
# BaseCall(name,molecule,Egys,CEgys,0,1,SuppressPrint,itr,**kwargs)
# if(lfrag.Iterate(itr)==0):
# done=True
# itr=itr+1
# lfrag.PrintEnergies(Egys,1,'Total Energy')
#
#
# def nmers(name,molecule,N,Egys,CEgys,SuppressPrint,**kwargs):
# lfrag.NMerHelper(N)
# PMan=Parallel()
# NStart=1
# NEnd=NStart
# while lfrag.GetNNMers(NEnd)!=0:
# NEnd+=1
# Egys.append([])
# for k,v in CEgys.iteritems():
# CEgys[k].append([])
# BaseCall(name,molecule,Egys,CEgys,NStart,NEnd,SuppressPrint,0,**kwargs)
# for i in range(NStart,NEnd):
# lfrag.PrintEnergies(Egys,i+1,'Total Energy')
#
# def SystemEnergy(Egys,IsCorr):
# return lfrag.CalcEnergy(Egys,IsCorr)
|