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https://github.com/LCPQ/quantum_package
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Install resultsFile
This commit is contained in:
parent
1dd9257ab8
commit
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5
Makefile
5
Makefile
@ -44,6 +44,11 @@ emsl: EMSL_Basis
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binary:
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$(QPACKAGE_ROOT)/scripts/make_binary.sh
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resultsFile:
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$(info $(BLUE)===== Fetching resultsFile from the web ===== $(BLACK))
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@sleep 1
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$(QPACKAGE_ROOT)/scripts/install_resultsFile.sh
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EZFIO: bin/irpf90
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$(info $(BLUE)===== Fetching EZFIO from the web ===== $(BLACK))
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@sleep 1
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@ -4,10 +4,10 @@
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# Mon Jan 12 12:57:19 CET 2015
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BASE="EMSL_Basis_Set_Exchange_Local"
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URL="https://github.com/LCPQ/EMSL_Basis_Set_Exchange_Local/archive/master.tar.gz"
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URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
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${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/EMSL_Basis.tar.gz
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tar -zxf EMSL_Basis.tar.gz && rm EMSL_Basis.tar.gz ||exit 1
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mv EMSL_Basis_Set_Exchange_Local-master EMSL_Basis
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${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
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tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
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mv ${BASE}-master EMSL_Basis
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12
scripts/install_resultsFile.sh
Executable file
12
scripts/install_resultsFile.sh
Executable file
@ -0,0 +1,12 @@
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#!/bin/bash
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#
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# Installs the resultsFile Python library
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# Mon Jan 19 15:08:18 CET 2015
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URL="https://github.com/LCPQ/resultsFile/archive/master.tar.gz"
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${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/resultsFile.tar.gz
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tar -zxf resultsFile.tar.gz && rm resultsFile.tar.gz ||exit 1
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mv resultsFile-master resultsFile
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293
scripts/qp_convert.py
Executable file
293
scripts/qp_convert.py
Executable file
@ -0,0 +1,293 @@
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#!/usr/bin/env python
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import sys,os
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try:
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QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
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except:
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print "Error: QPACKAGE_ROOT environment variable not found."
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sys.exit(1)
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sys.path = [ QPACKAGE_ROOT+"/EZFIO/Python", QPACKAGE_ROOT+"/resultsFile" ]+sys.path
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from ezfio import ezfio
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import ezfio as ez
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print "EZFIO: ", os.path.dirname(ez.__file__)
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try:
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from resultsFile import *
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except:
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print "Error: resultsFile Python library not installed"
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sys.exit(1)
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def write_ezfioFile(res,filename):
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res.clean_uncontractions()
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ezfio.set_file(filename)
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# Electrons
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ezfio.set_electrons_elec_alpha_num(res.num_alpha)
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ezfio.set_electrons_elec_beta_num(res.num_beta)
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# Nuclei
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ezfio.set_nuclei_nucl_num(len(res.geometry))
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charge = []
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coord = []
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coord_x = []
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coord_y = []
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coord_z = []
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for a in res.geometry:
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charge.append(a.charge)
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if res.units == 'BOHR':
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coord_x.append(a.coord[0])
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coord_y.append(a.coord[1])
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coord_z.append(a.coord[2])
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else:
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coord_x.append(a.coord[0]/a0)
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coord_y.append(a.coord[1]/a0)
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coord_z.append(a.coord[2]/a0)
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ezfio.set_nuclei_nucl_charge(charge)
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label = map(lambda x: x.name, res.geometry)
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ezfio.set_nuclei_nucl_label(label)
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ezfio.set_nuclei_nucl_coord(coord_x+coord_y+coord_z)
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# Basis
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basis = res.uncontracted_basis
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geom = res.geometry
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# MO
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MoTag = res.determinants_mo_type
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ezfio.set_mo_basis_mo_label('Orthonormalized')
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MO_type = MoTag
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allMOs = res.uncontracted_mo_sets[MO_type]
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closed = [ (allMOs[i].eigenvalue,i) for i in res.closed_mos ]
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active = [ (allMOs[i].eigenvalue,i) for i in res.active_mos ]
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virtual =[ (allMOs[i].eigenvalue,i) for i in res.virtual_mos ]
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# closed.sort()
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# active.sort()
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# virtual.sort()
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closed = map( lambda x: x[1], closed)
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active = map( lambda x: x[1], active)
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virtual = map( lambda x: x[1], virtual)
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MOindices = closed + active + virtual
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MOs = []
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for i in MOindices:
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MOs.append(allMOs[i])
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mo_tot_num = len(MOs)
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while len(MOindices) < mo_tot_num:
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MOindices.append(len(MOindices))
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MOmap = list(MOindices)
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for i in range(len(MOindices)):
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MOmap[i] = MOindices.index(i)
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energies = []
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for i in xrange(mo_tot_num):
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energies.append(MOs[i].eigenvalue)
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if res.occ_num is not None:
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OccNum = []
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for i in MOindices:
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OccNum.append(res.occ_num[MO_type][i])
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while len(OccNum) < mo_tot_num:
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OccNum.append(0.)
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MoMatrix = []
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sym0 = [ i.sym for i in res.mo_sets[MO_type] ]
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sym = [ i.sym for i in res.mo_sets[MO_type] ]
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for i in xrange(len(sym)):
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sym[MOmap[i]] = sym0[i]
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MoMatrix = []
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for i in xrange(len(MOs)):
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m = MOs[i]
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for coef in m.vector:
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MoMatrix.append(coef)
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while len(MoMatrix) < len(MOs[0].vector)**2:
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MoMatrix.append(0.)
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ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
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ezfio.set_mo_basis_mo_occ(OccNum)
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res.clean_contractions()
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# AO Basis
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import string
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at = []
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num_prim = []
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magnetic_number = []
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angular_number = []
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power_x = []
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power_y = []
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power_z = []
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coefficient = []
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exponent = []
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res.convert_to_cartesian()
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for b in res.basis:
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c = b.center
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for i,atom in enumerate(res.geometry):
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if atom.coord == c:
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at.append(i+1)
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num_prim.append(len(b.prim))
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s = b.sym
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power_x.append( string.count(s,"x") )
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power_y.append( string.count(s,"y") )
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power_z.append( string.count(s,"z") )
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coefficient.append( b.coef )
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exponent.append( [ p.expo for p in b.prim ] )
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ezfio.set_ao_basis_ao_num(len(res.basis))
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ezfio.set_ao_basis_ao_nucl(at)
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ezfio.set_ao_basis_ao_prim_num(num_prim)
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ezfio.set_ao_basis_ao_power(power_x+power_y+power_z)
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prim_num_max = ezfio.get_ao_basis_ao_prim_num_max()
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len_res_basis = len(res.basis)
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for i in range(len(res.basis)):
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coefficient[i] += [ 0. for j in range(len(coefficient[i]),prim_num_max) ]
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exponent[i] += [ 0. for j in range(len(exponent[i]),prim_num_max) ]
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coefficient = reduce(lambda x, y: x+y, coefficient, [])
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exponent = reduce(lambda x, y: x+y, exponent, [])
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coef = []
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expo = []
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for i in range(prim_num_max):
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for j in range(i,len(coefficient),prim_num_max):
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coef.append ( coefficient[j] )
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expo.append ( exponent[j] )
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ezfio.set_ao_basis_ao_coef(coef)
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ezfio.set_ao_basis_ao_expo(expo)
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ezfio.set_ao_basis_ao_basis("Read by resultsFile")
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# Apply threshold to determinants
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if len(res.determinants) == 1:
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sorted_determinants = [ (-1.,1.,res.determinants[0]) ]
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else:
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sorted_determinants = []
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for i,j in zip(res.det_coefficients[0],res.determinants):
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sorted_determinants.append((-abs(i),i,j))
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sorted_determinants.sort()
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norm = 0.0
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for length, (a,b,c) in enumerate(sorted_determinants):
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if -a < det_threshold:
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length -=1
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break
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norm += a**2
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norm = sqrt(norm)
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length += 1
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for i in xrange(length):
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a = sorted_determinants[i]
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sorted_determinants[i] = (a[0],a[1]/norm,a[2])
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sorted_determinants = sorted_determinants[:length]
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# MOs
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mo_tot_num = len(res.mo_sets[MoTag])
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closed_mos = res.closed_mos
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active_mos = res.active_mos
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virtual_mos = res.virtual_mos
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to_remove = []
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to_add = []
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for i in active_mos:
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found = False
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for (a,b,c) in sorted_determinants:
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if i in c['alpha']+c['beta']:
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found = True
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break
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if not found:
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to_remove.append(i)
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to_add.append(i)
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virtual_mos = to_add + virtual_mos
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for i in active_mos:
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always = True
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for (a,b,c) in sorted_determinants:
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if not (i in c['alpha'] and i in c['beta']):
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always = False
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break
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if always:
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to_remove.append(i)
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closed_mos.append(i)
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for i in to_remove:
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active_mos.remove(i)
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MOindices = closed_mos + active_mos + virtual_mos
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while len(MOindices) < mo_tot_num:
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MOindices.append(len(MOindices))
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MOmap = list(MOindices)
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for i in range(len(MOindices)):
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MOmap[i] = MOindices.index(i)
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ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
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mo = []
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for i in MOindices:
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mo.append(res.mo_sets[MoTag][i])
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if len(mo) < mo_tot_num:
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newmo = orbital()
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newmo.eigenvalue = 0.
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newmo.vector = [0. for i in range(mo_tot_num)]
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newmo.vector[len(mo)] = 1.
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while len(mo) < mo_tot_num:
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mo.append(newmo)
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Energies = [ m.eigenvalue for m in mo ]
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if res.occ_num is not None:
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OccNum = []
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for i in MOindices:
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OccNum.append(res.occ_num[MoTag][i])
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while len(OccNum) < mo_tot_num:
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OccNum.append(0.)
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ezfio.set_mo_basis_mo_occ(OccNum)
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cls = [ "v" for i in mo ]
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for i in closed_mos:
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cls[MOmap[i]] = 'c'
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for i in active_mos:
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cls[MOmap[i]] = 'a'
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sym0 = [ i.sym for i in res.mo_sets[MoTag] ]
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sym = [ i.sym for i in res.mo_sets[MoTag] ]
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for i in xrange(len(sym)):
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sym[MOmap[i]] = sym0[i]
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MoMatrix = []
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for m in mo:
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for coef in m.vector:
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MoMatrix.append(coef)
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while len(MoMatrix) < len(mo[0].vector)**2:
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MoMatrix.append(0.)
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ezfio.set_mo_basis_mo_coef(MoMatrix)
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del MoMatrix
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if __name__ == '__main__':
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# Check command line
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det_threshold = 0.
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if len(sys.argv) == 2:
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State=0
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elif len(sys.argv) == 3:
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State=int(sys.argv[2])
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else:
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print "usage: "+sys.argv[0]+" file.out [state]"
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sys.exit(2)
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firstArg = sys.argv[1]
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file = getFile(firstArg)
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print firstArg, 'recognized as', str(file).split('.')[-1].split()[0]
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filename = firstArg+".ezfio"
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write_ezfioFile(file,filename)
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@ -47,7 +47,7 @@ source quantum_package.rc
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make EZFIO
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if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
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then
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echo $RED "Error in IRPF90 installation" $BLACK
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echo $RED "Error in EZFIO installation" $BLACK
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exit 1
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fi
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@ -58,6 +58,14 @@ then
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exit 1
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fi
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make resultsFile
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if [[ ! -d ${QPACKAGE_ROOT}/resultsFile ]]
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then
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echo $RED "Error in resultsFile installation" $BLACK
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exit 1
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fi
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echo $RED "
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=======================================================
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To complete the installation, add the following line to
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