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Documentation
This commit is contained in:
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7
Makefile
7
Makefile
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VERSION=1.1
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default:
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- rm -rf build dist
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- export VERSION=$(VERSION) ;\
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./setup.py --quiet bdist_rpm
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- sudo rpm -e resultsFile
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- sudo rpm -hiv dist/resultsFile*.noarch.rpm
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138
README.md
138
README.md
@ -1,2 +1,140 @@
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# resultsFile
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Python interface to read output files of quantum chemistry programs
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To add a module to read a new kind of output file, just add a file
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in the `Modules` directory.
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# Using the library
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Example (`resultsFile` is supposed to be in your `sys.path`):
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``` Python
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import resultsFile
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file = resultsFile.getFile("g09_output.log")
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print 'recognized as', str(file).split('.')[-1].split()[0]
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print file.mo_sets
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```
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## Constraints
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### Gaussian09
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* `GFPRINT` : Needed to read the AO basis set
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* `pop=Full` : Needed to read all the MOs
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* `#p CAS(SlaterDet)` : CAS-SCI CI coefficients
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When doing a CAS with Gaussian, first do the Hartree-Fock calculation saving the checkpoint
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file and then do the CAS in a second calculation.
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### Molpro
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* `print, basis;` : Needed to read the AO basis set
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* `gprint,orbital;` : Needed to read the MOs
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* `gprint,civector; gthresh,printci=0.;` : Needed to read the CI coefficients
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* `orbprint` : Ensures all the MOs are printed
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An RHF calculation is mandatory before any MCSCF calculation, since some
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information is printed only the RHF section. Be sure to print *all* molecular
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orbitals using the `orbprint` keyword, and to use the same spin multiplicity
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and charge between the RHF and the CAS.
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### GAMESS-US
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For MCSCF calculations, first compute the MCSCF single-point wave function with
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the GUGA algorithm. Then, put the the MCSCF orbitals (of the `.dat` file) in
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the GAMESS input file, and run a single-point GUGA CI calculation with the
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following keywords:
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* `PRTTOL=0.0001` in the `$GUGDIA` group to use a threshold of 1.E-4 on the CI coefficients
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* `NPRT=2` in the `$CIDRT` group to print the CSF expansions in terms of Slater determinants
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* `PRTMO=.T.` in the `$GUESS` group to print the molecular orbitals
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# Debugging
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Any module can be run as an stand-alone executable. For example:
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```
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$ resultsFile/Modules/gamessFile.py
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resultsFile version 1.0, Copyright (C) 2007 Anthony SCEMAMA
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resultsFile comes with ABSOLUTELY NO WARRANTY; for details see the
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gpl-license file.
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This is free software, and you are welcome to redistribute it
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under certain conditions; for details see the gpl-license file.
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Usage:
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------
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resultsFile/Modules/gamessFile.py [options] file
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Options:
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--------
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--date : When the calculation was performed.
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--version : Version of the code generating the file.
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--machine : Machine where the calculation was run.
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--memory : Requested memory for the calculation.
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--disk : Requested disk space for the calculation.
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--cpu_time : CPU time.
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--author : Who ran the calculation.
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--title : Title of the run.
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--units : Units for the geometry (au or angstroms).
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--methods : List of calculation methods.
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--options : Options given in the input file.
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--spin_restrict : Open-shell or closed-shell calculations.
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--conv_threshs : List of convergence thresholds.
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--energies : List of energies.
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--one_e_energies : List of one electron energies.
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--two_e_energies : List of two electron energies.
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--ee_pot_energies : List of electron-electron potential energies.
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--Ne_pot_energies : List of nucleus-electron potential energies.
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--pot_energies : List of potential energies.
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--kin_energies : List of kinetic energies.
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--virials : Virial ratios.
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--point_group : Symmetry used.
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--num_elec : Number of electrons.
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--charge : Charge of the system.
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--multiplicity : Spin multiplicity of the system.
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--nuclear_energy : Repulsion of the nuclei.
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--dipole : Dipole moment
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--geometry : Atom types and coordinates.
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--basis : Basis set definition
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--mo_sets : List of molecular orbitals
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--mo_types : Types of molecular orbitals (canonical, natural,...)
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--mulliken_mo : Mulliken atomic population in each MO.
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--mulliken_ao : Mulliken atomic population in each AO.
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--mulliken_atom : Mulliken atomic population.
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--lowdin_ao : Lowdin atomic population in each AO.
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--mulliken_atom : Mulliken atomic population.
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--lowdin_atom : Lowdin atomic population.
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--two_e_int_ao : Two electron integrals in AO basis
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--determinants : List of Determinants
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--num_alpha : Number of Alpha electrons.
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--num_beta : Number of Beta electrons.
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--closed_mos : Closed shell molecular orbitals
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--active_mos : Active molecular orbitals
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--virtual_mos : Virtual molecular orbitals
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--determinants_mo_type : MO type of the determinants
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--det_coefficients : Coefficients of the determinants
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--csf_mo_type : MO type of the determinants
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--csf_coefficients : Coefficients of the CSFs
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--symmetries : Irreducible representations
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--occ_num : Occupation numbers
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--csf : List of Configuration State Functions
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--num_states : Number of electronic states
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--two_e_int_ao_filename :
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--one_e_int_ao_filename :
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--atom_to_ao_range :
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--gradient_energy : Gradient of the Energy wrt nucl coord.
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--text :
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--uncontracted_basis :
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--uncontracted_mo_sets :
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```
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File diff suppressed because it is too large
Load Diff
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#!/usr/bin/python
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# resultsFile is a library which allows to read output files of quantum
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# chemistry codes and write input files.
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# Copyright (C) 2007 Anthony SCEMAMA
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation; either version 2 of the License, or
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# (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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#
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# Anthony Scemama
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# LCPQ - IRSAMC
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# Universite Paul Sabatier
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# 118, route de Narbonne
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# 31062 Toulouse Cedex 4
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# scemama@irsamc.ups-tlse.fr
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import include
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eval(include.code)
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import struct
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import re
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import os
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QMCCHEM_PATH = os.getenv("QMCCHEM_PATH",default="")
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if QMCCHEM_PATH == "":
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print "QmcChem new files are not handled."
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class qmcchem_newFile(resultsFile):
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pass
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else:
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sys.path = [ QMCCHEM_PATH+"/scripts" ]+sys.path
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from ezfio import ezfio
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qmcchem_newFile_defined_vars = [ "date", "version", \
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"title", "units", "methods", \
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"point_group", "num_elec", \
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"charge", "multiplicity","geometry",\
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"basis","mo_sets","mo_types",\
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"determinants", "num_alpha", "num_beta",\
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"closed_mos", "active_mos", "virtual_mos", \
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"determinants_mo_type", "det_coefficients", \
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"csf_mo_type", "csf_coefficients", "occ_num", \
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"csf" ]
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class qmcchem_newFile(resultsFile):
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""" Class defining the qmcchem_new file.
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"""
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local_vars = list(local_vars)
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defined_vars = list(qmcchem_newFile_defined_vars)
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def __init__(self,name):
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resultsFile.__init__(self,name)
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ezfio.set_filename(self.filename)
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def get_version(self):
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if self._version is None:
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self._version = ezfio.get_version()
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return self._version
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def get_date(self):
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if self._date is None:
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self._date = ezfio.get_ezfio_creation()
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return self._date
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def get_num_elec(self):
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if self._num_elec is None:
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self._num_elec = self.num_alpha + self.num_beta
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return self._num_elec
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def get_multiplicity(self):
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if self._multiplicity is None:
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self._multiplicity = self.num_alpha - self.num_beta + 1
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return self._multiplicity
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def get_charge(self):
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if self._charge is None:
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self._charge = sum(ezfio.get_nuclei_nucl_charge())-float(self.num_elec)
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return self._charge
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def get_title(self):
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if self._title is None:
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self._title = self.filename
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return self._title
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def get_units(self):
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if self._units is None:
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self._units = 'BOHR'
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#for a gamess use the units is give by an option on gamess_write_contrl
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return self._units
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def get_methods(self):
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if self._methods is None:
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self._methods = ['QMC']
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return self._methods
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def get_point_group(self):
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if self._point_group is None:
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self._point_group = "C1"
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return self._point_group
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def get_geometry(self):
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if self._geometry is None:
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self.get_geometryX()
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self.get_basisX()
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return self._geometry
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def get_basis(self):
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if self._basis is None:
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self.get_geometry()
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return self._basis
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def get_geometryX(self):
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self._geometry = []
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charge = ezfio.get_nuclei_nucl_charge()
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coord = ezfio.get_nuclei_nucl_coord()
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num = ezfio.get_nuclei_nucl_num()
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for i in range(num):
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temp = atom()
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temp.charge = charge[i]
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temp.coord = (coord[0][i], coord[1][i], coord[2][i])
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temp.name = 'X'
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temp.basis = []
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self._geometry.append(temp)
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def get_basisX(self):
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coef = ezfio.get_ao_basis_ao_coef()
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expo = ezfio.get_ao_basis_ao_expo()
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nucl = ezfio.get_ao_basis_ao_nucl()
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num = ezfio.get_ao_basis_ao_num()
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power= ezfio.get_ao_basis_ao_power()
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prim_num= ezfio.get_ao_basis_ao_prim_num()
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self._basis = []
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for i in range(num):
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contr = contraction()
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for j in range(prim_num[i]):
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gauss = gaussian()
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atom = self._geometry[nucl[i]-1]
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gauss.center = atom.coord
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gauss.expo = expo[j][i]
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name = normalize_basis_name('x'*power[0][i]+'y'*power[1][i]+'z'*power[2][i])
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if name == '': name = 's'
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gauss.sym = name
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contr.append(coef[j][i],gauss)
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self._geometry[nucl[i]-1].basis.append(contr)
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self._basis.append(contr)
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def get_mo_types(self):
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if self._mo_types is None:
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self._mo_types = ['QMC']
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return self._mo_types
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def get_mo_sets(self):
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if self._mo_sets is None:
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self._mo_sets = {}
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self._mo_sets['QMC'] = []
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coef = ezfio.get_mo_basis_mo_coef()
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energy = ezfio.get_mo_basis_mo_energy()
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num = ezfio.get_mo_basis_mo_tot_num()
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for i in range(num):
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v = orbital()
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v.basis = self.basis
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v.set = 'QMC'
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v.eigenvalue = energy[i]
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v.vector = coef[i]
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self.mo_sets['QMC'].append(v)
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return self._mo_sets
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def get_num_alpha(self):
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if self._num_alpha is None:
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self._num_alpha = ezfio.get_electrons_elec_alpha_num()
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return self._num_alpha
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def get_num_beta(self):
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if self._num_beta is None:
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self._num_beta = ezfio.get_electrons_elec_beta_num()
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return self._num_beta
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def get_determinants_mo_type(self):
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if self._determinants_mo_type is None:
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self._determinants_mo_type = 'QMC'
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return self._determinants_mo_type
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def get_csf_mo_type(self):
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if self._csf_mo_type is None:
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self._csf_mo_type = 'QMC'
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return self._csf_mo_type
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def get_determinants(self):
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if self._determinants is None:
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determinants = []
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if self.csf is not None:
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for csf in self.csf:
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for new_det in csf.determinants:
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determinants.append(new_det)
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else:
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pass
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if determinants != []:
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self._determinants_mo_type = self.mo_types[-1]
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self._determinants = determinants
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return self._determinants
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def get_csf(self):
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method = self.methods[0]
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if self._csf is None:
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csf = []
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ncore = ezfio.get_mo_basis_mo_closed_num()
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nact = ezfio.get_mo_basis_mo_active_num()
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core_a = []
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core_b = []
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for i in range(ncore):
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core_a.append(i)
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core_b.append(i)
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num = ezfio.get_determinants_det_num()
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occ = ezfio.get_determinants_det_occ()
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if occ == []:
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occ = [[[0]],[[0]]]
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for i in range(num):
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this_csf = CSF()
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tempcsf_a = core_a + map(lambda x: x-1, occ[0][i])
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tempcsf_b = core_b + map(lambda x: x-1, occ[1][i])
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this_csf.append(1.,tempcsf_a,tempcsf_b)
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csf.append(this_csf)
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if csf != []:
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self._csf = csf
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return self._csf
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def get_closed_mos(self):
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if self._closed_mos is None:
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cls = ezfio.get_mo_basis_mo_classif()
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self._closed_mos = []
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self._virtual_mos = []
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self._active_mos = []
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for i in range(len(cls)):
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if cls[i] == 'c':
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self._closed_mos.append(i)
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elif cls[i] == 'a':
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self._active_mos.append(i)
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elif cls[i] == 'v':
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self._virtual_mos.append(i)
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return self._closed_mos
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def get_virtual_mos(self):
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if self._virtual_mos is None:
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self.get_closed_mos()
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return self._virtual_mos
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def get_active_mos(self):
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if self._active_mos is None:
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self.get_closed_mos()
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return self._active_mos
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def get_det_coefficients(self):
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if self._det_coefficients is None:
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self._det_coefficients = []
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csf = self.csf
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for state_coef in self.csf_coefficients:
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vector = []
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for i,c in enumerate(state_coef):
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for d in csf[i].coefficients:
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vector.append(c*d)
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self._det_coefficients.append(vector)
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return self._det_coefficients
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def get_csf_coefficients(self):
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if self._csf_coefficients is None:
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self._csf_coefficients = [ [] ]
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self._csf_coefficients[0] = ezfio.get_determinants_det_coef()
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return self._csf_coefficients
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def get_occ_num(self):
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if self._occ_num is None:
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self._occ_num = {}
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motype = 'QMC'
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self._occ_num[motype] = ezfio.get_mo_basis_mo_occ()
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return self._occ_num
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fileTypes.append(qmcchem_newFile)
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if __name__ == '__main__':
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main(qmcchem_newFile)
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