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Moved from C++ to C. Updated Python files.

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This commit is contained in:
Adam Parler 2023-12-06 02:37:36 -08:00 • committed by Adam Parler
parent 02608cf25a
commit 8663962fcf
7 changed files with 270 additions and 149 deletions
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7
.gitignore vendored
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@ -1,3 +1,8 @@
.vscode
bin/
build/
include/
lib/
### C ###
# Prerequisites
@ -19,7 +24,6 @@
*.gch
*.pch
# Libraries
*.dll
*.so
@ -89,6 +93,7 @@ ehthumbs_vista.db
# Folder config file
Desktop.ini
.DS_Store
# Recycle Bin used on file shares
$RECYCLE.BIN/

63
src/basis/getlibr.py Normal file → Executable file
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@ -1,26 +1,35 @@
#!/usr/bin/env python3
#!/usr/bin/python3
# This script downloads the basis set library data from www.basissetexchange.org
# into the directory $NWCHEM_TOP/src/basis/libraries.bse
# to use, set the env. variable NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/src/basis/libraries.bse/
# To run, cd $NWCHEM_TOP/src/basis/libraries.bse/ && ../getlibr.py
# this will update the content of $NWCHEM_TOP/src/basis/libraries.bse
# To use the updates library, set the env. variable NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/src/basis/libraries.bse/
# Requires the installation of the python env. from
# https://github.com/MolSSI-BSE/basis_set_exchange
# e.g. python3 -m pip install --user basis_set_exchange
# See https://molssi-bse.github.io/basis_set_exchange/
#
# names changed
# def2-universal-jfit was weigend_coulomb_fitting
# dgauss-a1-dftjfit was dgauss_a1_dft_coulomb_fitting
# dgauss-a2-dftjfit was dgauss_a2_dft_coulomb_fitting
#
import basis_set_exchange as bse
from datetime import datetime
today = datetime.now().isoformat(timespec='minutes')
print(today)
all_bs = bse.get_all_basis_names()
md = bse.get_metadata()
for bas_name in all_bs:
#get version and list of elements
version_bs = md[bas_name]['latest_version']
elements_list = md[bas_name]['versions'][version_bs]['elements']
summary_file = open('summary.txt','w')
def writebs(md, bas_name, summary_file, get_aux=0):
md_bas_name = bas_name.lower()
md_bas_name = md_bas_name.replace("*","_st_")
md_bas_name = md_bas_name.replace("/","_sl_")
print(' md_bas_name '+md_bas_name+"\n")
print(' bas_name '+bas_name+"\n")
version_bs = md[md_bas_name]['latest_version']
elements_list = md[md_bas_name]['versions'][version_bs]['elements']
#open file
# get rid of asterisks
file_name = bas_name.replace("*","s")
@ -33,19 +42,38 @@ for bas_name in all_bs:
file_name = file_name.replace(" ","_")
#replace forward slash with underscore
file_name = file_name.replace("/","_")
#lowercase
file_name = file_name.lower()
if get_aux==1:
file_name = file_name + "-autoaux"
print(' file name is '+file_name+"\n")
output_file = open(file_name,'w')
output_file.write('# BSE Version '+bse.version()+'\n')
output_file.write('# Data downloaded at '+today+'\n')
output_file.write('# Data downloaded on '+today+'\n')
if get_aux==0:
output_file.write('# '+bas_name+' version number '+version_bs+'\n')
output_file.write('# Description: '+md[bas_name]['description']+'\n')
output_file.write('# Role: '+md[bas_name]['role']+'\n')
output_file.write('# Description: '+md[md_bas_name]['description']+'\n')
output_file.write('# Role: '+md[md_bas_name]['role']+'\n')
output_file.write('# '+bse.get_references(bas_name,fmt='txt').replace('\n','\n# '))
output_file.write('# \n')
elif get_aux==1:
output_file.write('# '+bas_name+' version number '+version_bs+' AutoAux \n')
output_file.write('# Role: JK Fitting \n')
output_file.write('# Stoychev GL, Auer AA, Neese F. \n# Automatic Generation of Auxiliary Basis Sets.\n# J Chem Theory Comput. 2017 Feb 14;13(2):554-562.\n# doi: 10.1021/acs.jctc.6b01041.\n')
output_file.write('# \n')
n_elements=0
for element in elements_list:
n_elements = n_elements + 1
if get_aux==1:
summary_file.write('Basis set \"'+bas_name+'-autoaux\" (number of atoms '+str(n_elements)+')\n')
else:
summary_file.write('Basis set \"'+bas_name+'\" (number of atoms '+str(n_elements)+')\n')
for element in elements_list:
#element='h'
try:
bs_str=bse.get_basis(bas_name, header=False, elements=element, fmt='nwchem', optimize_general=True, uncontract_general=True)
bs_str=bse.get_basis(bas_name, header=False, elements=element, fmt='nwchem', optimize_general=True, uncontract_general=True, get_aux=get_aux)
except:
# print("failed for"+element)
pass
@ -54,11 +82,22 @@ for bas_name in all_bs:
bs_str=bs_str.replace("END","end")
bs_str=bs_str.replace("PRINT","")
element_str=bse.misc.compact_elements([element])
if get_aux==1:
bs_str=bs_str.replace("ao basis",element_str+"_"+bas_name+"-autoaux")
else:
bs_str=bs_str.replace("ao basis",element_str+"_"+bas_name)
#ECP
bs_str=bs_str.replace("ECP","ecp \""+element_str+"_"+bas_name+"\"")
output_file.write(bs_str)
#
print(bas_name+" "+element_str)
print("end")
return
for bas_name in all_bs:
md_bas_name = bas_name.lower()
md_bas_name = md_bas_name.replace("*","_st_")
md_bas_name = md_bas_name.replace("/","_sl_")
writebs(md, bas_name, summary_file)
if md[md_bas_name]['role'] == 'orbital':
writebs(md, bas_name, summary_file, get_aux=1)
print("end")

0
src/nwchem.cpp → src/nwchem.c
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288
src/rtdb/rtdb.h
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@ -1,105 +1,183 @@
//
// Header file for intial FORTRAN interface to RTDB
// (see the C header file rtdb.h for more detail)
//
// All functions return .TRUE. on success, .FALSE. on failure
//
// All functions are also mirrored by routines rtdb_* -> rtdb_par_*
// in which process 0 performs the operation and all other processes
// are broadcast the result of a read and discard writes.
//
// rtdb_max_key ... an integer parameter that defines the maximum
// length of a character string key
//
// rtdb_max_file ... an integer parameter that defines the maximum
// length of a file name
//
//
// logical function rtdb_parallel(mode)
// logical mode [input]
//
//
// logical function rtdb_open(filename, mode, handle)
// character *(*) filename [input]
// character *(*) mode [input]
// integer handle [output]
//
// logical function rtdb_clone(handle, suffix)
// integer handle [input]
// character*(*) suffix [input]
//
// logical function rtdb_close(handle, mode)
// integer handle [input]
// character*(*) mode [input]
//
// logical function rtdb_put(handle, name, ma_type, nelem, array)
// integer handle [input]
// character *(*) name [input]
// integer ma_type [input]
// integer nelem [input]
// <ma_type>array(nelem) [input]
//
// logical function rtdb_get_info(handle, name, ma_type, nelem, date)
// integer handle [input]
// character *(*) name [input]
// integer ma_type [output]
// integer nelem [output]
// character*26 date [output]
//
// logical function rtdb_get(handle, name, ma_type, nelem, array)
// integer handle [input]
// character *(*) name [input]
// integer ma_type [input]
// integer nelem [input]
// <ma_type>array(nelem) [output]
//
// logical function rtdb_ma_get(handle, name, ma_type, nelem, ma_handle)
// integer handle [input]
// character *(*) name [input]
// integer ma_type [output]
// integer nelem [output]
// integer ma_handle [output]
//
// logical function rtdb_cput(handle, name, nelem, buf)
// integer handle [input]
// character *(*) name [input]
// character *(*) buf [input]
//
// logical function rtdb_cget(handle, name, nelem, buf)
// integer handle [input]
// character *(*) name [input]
// character *(*) buf [output]
//
// logical function rtdb_print(handle, print_values)
// integer handle [input]
// logical print_values [input]
//
// logical function rtdb_first(handle, name)
// integer handle [input]
// character *(*) name [output]
//
// logical function rtdb_next(handle, name)
// integer handle [input]
// character *(*) name [output]
//
// logical function rtdb_delete(handle, name)
// integer handle [input]
// character *(*) name [input]
//
bool rtdb_open, rtdb_close, rtdb_put, rtdb_get, rtdb_ma_get,
rtdb_cput, rtdb_cget, rtdb_print, rtdb_get_info,
rtdb_first, rtdb_next, rtdb_delete, rtdb_parallel,
rtdb_clone,rtdb_getfname,rtdb_cget_size;
//$Id$
extern rtdb_open, rtdb_close, rtdb_put, rtdb_get, rtdb_ma_get,
rtdb_cput, rtdb_cget, rtdb_print, rtdb_get_info,
rtdb_first, rtdb_next, rtdb_delete, rtdb_parallel,
rtdb_clone,rtdb_getfname,rtdb_cget_size;
//
// Check these values against rtdb_f2c.c
//
const int rtdb_max_key=255;
const int rtdb_max_file=255;
//
const bool rtdb_seq_mode = false;
const bool rtdb_par_mode = true;
#ifndef _RTDB_H
#define _RTDB_H
/*
All routines return TRUE (1) on success, FALSE (0) on failure.
int rtdb_parallel(const int mode)
Set the parallel access mode of all databases to mode and
return the previous setting
int rtdb_open(const char *filename, const char *mode, int *handle)
Filename = path to file associated with the data base
mode = 'new' Open only if it does not exist already
'old', Open only if it does exist already
'unknown' Create new or open existing (preserving contents)
'empty' Create new or open existing (deleting contents)
'scratch' Create new or open existing (deleting contents)
and automatically delete upon closing. Also, items
cached in memory are not written to disk.
handle = returns handle by which all future references to the
data base are made
int rtdb_clone(const int handle, const char *suffix)
Copy the data base file
handle = handle to RTDB
suffix
int rtdb_close(const int handle, const char *mode)
Close the data base
handle = handle to RTDB
mode = 'keep' Preserve the data base file to enable restart
'delete' Delete the data base file freeing all resources
mode is overridden by opening the data base with
mode='scratch' in which instance it is always deleted
upon closing
int rtdb_get_info(const int handle, const char *name, int *ma_type,
int *nelem, char date[26])
Get info about an entry from the data base
handle = handle to RTDB
name = entry name (null terminated character string)
ma_type = returns MA type of the entry
nelem = returns no. of elements of the given type
date = returns date of insertion (null terminated character string)
int rtdb_put(const int handle, const char *name, const int ma_type,
const int nelem, const void *array)
Insert an entry into the data base replacing previous entry
handle = handle to RTDB
name = entry name (null terminated character string)
ma_type = MA type of the entry
nelem = no. of elements of the given type
array = data to be inserted
int rtdb_get(const int handle, const char *name, const int ma_type,
const int nelem, void *array)
Get an entry from the data base
handle = handle to RTDB
name = entry name (null terminated character string)
ma_type = MA type of the entry which must match entry type
nelem = size of array in units of ma_type
array = user provided buffer that returns data
int rtdb_ma_get(const int handle, const char *name, int *ma_type,
int *nelem, int *ma_handle)
Get an entry from the data base returning an MA handle
handle = handle to RTDB
name = entry name (null terminated character string)
ma_type = returns MA type of the entry
nelem = returns no. of elements of type ma_type in data
ma_handle= returns MA handle to data
int rtdb_first(const int handle, const int namelen, char *name)
Return the name of the first (user inserted) entry in the data base.
The order is effectively random.
handle = handle to RTDB
namelen = size of user provided buffer name
name = name of entry is returned in this buffer
int rtdb_next(const int handle, const int namelen, char *name)
Return the name of the next (user inserted) entry in the data base.
The order is effectively random.
handle = handle to RTDB
namelen = size of user provided buffer name
name = name of entry is returned in this buffer
int rtdb_print(const int handle, const int print_values)
Print the contents of the data base to stdout
handle = handle to RTDB
print_values = boolean flag ... if true values as well as
keys are printed out.
int rtdb_delete(const int handle, const char *name)
Delete the entry from the database.
Return
1 if key was present and successfully deleted
0 if key was not present, or if an error occured
handle = handle to RTDB
name = name of entry to delete
*/
int rtdb_open(const char *, const char *, int *);
int rtdb_clone(const int, const char *);
int rtdb_getfname(const int, char [36]);
int rtdb_close(const int, const char *);
int rtdb_put(const int, const char *, const int, const int,
const void *);
int rtdb_get(const int, const char *, const int, const int,
bool);
int rtdb_get_info(const int, const char *, int *, int *, char [26]);
int rtdb_ma_get(const int, const char *, int *, int *, int *);
int rtdb_first(const int, const int, char *);
int rtdb_next(const int, const int, char *);
int rtdb_print(const int, const int);
int rtdb_delete(const int, const char *);
int rtdb_parallel(const int);
/*
Following are 'sequential' versions of the above
for internal use only
*/
int rtdb_seq_open(const char *, const char *, int *);
int rtdb_seq_copy(const int, const char *);
int rtdb_seq_getfname(const int, char [36]);
int rtdb_seq_close(const int, const char *);
int rtdb_seq_put(const int, const char *, const int, const int,
const void *);
int rtdb_seq_get(const int, const char *, const int, const int,
void *);
int rtdb_seq_get_info(const int, const char *, int *, int *, char [26]);
int rtdb_seq_ma_get(const int, const char *, int *, int *, int *);
int rtdb_seq_first(const int, const int, char *);
int rtdb_seq_next(const int, const int, char *);
int rtdb_seq_print(const int, const int);
int rtdb_seq_delete(const int, const char *);
#define RTDB_SEQ_MODE 0 //* Sequential mode
#define RTDB_PAR_MODE 1 //* Parallel mode
#if (defined(CRAY) || defined(WIN32)) &&!defined(__crayx1) &&!defined(__MINGW32__)
#include "rtdb.cray.h"
#endif
#endif

22
src/tce/oce.py
View file

@ -27,7 +27,7 @@ def stringtooperatorsequence(expression):
"""Converts a string to an operatorsequence object"""
# Syntax of the string is rather loosely defined as:
# (1) Numerical factor (with no permutation allowed) (optional), summation (optional), amplitudes (optional), normal ordered sequence,
# (2) Numerical factor can be an arithmatic expression such as (1.0/4.0),
# (2) Numerical factor can be an arithmetic expression such as (1.0/4.0),
# (3) Summation starts with either "SUM" or "sum" followed by a parenthesis of indexes,
# (4) Indexes can be either in one-letter notation (a-h, A-H for virtuals, i-o, I-O for occupieds, p-z, P-Z for either, case matters)
# or in OCE notation (p1,p2 for virtuals, h3,h4 for occupieds, g5,g6 for either, no overlap in numbering)
@ -71,8 +71,7 @@ def stringtooperatorsequence(expression):
elif (index[0] == "g"):
newsequence.append(Operator("general",dagger,int(index[1:])))
else:
print("Syntax error: an operator not recognized")
stop
raise SyntaxError(" an operator not recognized")
operatorlist = operatorlist + newsequence
newsequences.append(newsequence)
@ -156,8 +155,7 @@ def stringtooperatorsequence(expression):
summation.indexes.append(indexinthelist)
break
else:
print("syntax error")
stop
raise SyntaxError(" ")
# get amplitudes
remainder = string.split(remainder,")")
@ -221,8 +219,7 @@ def stringtooperatorsequence(expression):
newamplitude.indexes.append(indexinthelist)
break
else:
print("syntax error")
stop
raise SyntaxError(" ")
amplitudes.append(newamplitude)
newoperatorsequence = OperatorSequence(numericalfactor,summation,amplitudes,newsequences)
@ -231,8 +228,7 @@ def stringtooperatorsequence(expression):
def combinepermutations(one,two):
"""Connects two permutations of indexes"""
if (len(one) != len(two)):
print("Internal error")
stop
raise SyntaxError(" ")
three = []
for n in range(len(one)/2):
three.append(one[n])
@ -749,7 +745,7 @@ class Factor:
raise RuntimeError("unrealistic factor")
fraction = abs(int(1.0/coefficient))
if (1.0/float(fraction) != abs(coefficient)):
print(" !!! WARNING !!! inaccurate arithmatic")
print(" !!! WARNING !!! inaccurate arithmetic")
if (fraction == 1):
frac = ""
else:
@ -1732,7 +1728,7 @@ class ListOperatorSequences:
print("")
for line in self.show():
print(line)
return ""
return""
def show(self):
"""Returns a human-friendly string of the content"""
@ -1813,7 +1809,7 @@ class ListOperatorSequences:
# pick up a pair of operator sequences
for nsequencea in range(len(self.list)):
# if (verbose):
# print('processing ',nsequencea,' / ',range(len(self.list)))
# print 'processing ',nsequencea,' / ',range(len(self.list))
sequencea = self.list[nsequencea]
for nsequenceb in range(len(self.list)):
sequenceb = self.list[nsequenceb]
@ -1907,7 +1903,7 @@ class ListOperatorSequences:
print(" ! Warning! a cyclic contraction is found")
# self.simplifythree(verbose)
self.simplifytwo(verbose)
# the followings do not seem to affect the result, yet it costs enormous memory & time
# the following do not seem to affect the result, yet it costs enormous memory & time
# self.simplifyfour(1)
self = copy.deepcopy(self.deletezero())
return self

15
src/tce/splitfiles.py
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@ -1,10 +1,7 @@
#!/usr/bin/env python3
# Usage: python splitfiles.py < inputfile.F
# (c) All rights reserved by Battelle & Pacific Northwest Nat'l Lab (2002)
# $Id$
import string
import copy
import sys
source = sys.stdin.readlines()
@ -13,20 +10,22 @@ if (not source):
print("Usage: python splitfiles.py < inputfile.F")
nfiles = 0
filename = " "
filecontent = " "
for line in source:
if (string.find(line,"SUBROUTINE") != -1):
if (line.find("SUBROUTINE") != -1):
if (nfiles):
file = open(filename+".F","w")
file = open(filename+".F", "w")
for newline in filecontent:
file.write(newline)
filename = string.split(line[string.find(line,"SUBROUTINE")+11:],"(")[0]
filename = line[line.find("SUBROUTINE")+11:].split("(", 99999)[0]
print(filename+".o\\")
nfiles = nfiles + 1
filecontent = [line]
else:
filecontent.append(line)
# don't forget to dump the last subroutine
file = open(filename+".F","w")
file = open(filename+".F", "w")
for newline in filecontent:
file.write(newline)
print("Number of files generated:",nfiles)
print("Number of files generated:", nfiles)

6
src/util/errquit.h
View file

@ -1,6 +1,8 @@
#ifndef _ERRQUIT_H
#define _ERRQUIT_H
// UERR - Not yet assigned to a category
// UNKNOWN_ERR - Not yet assigned to a category
// MEM_ERROR - Generic Memory error
// MEM_ERR - Generic Memory error
// RTDB_ERR - Error in the Runtime Database
// INPUT_ERR - Error resulting from inproper user input
// CAPMIS_ERR - Features that have not been implemented yet
@ -31,3 +33,5 @@ const int DISK_ERR = 100;
const int CALC_ERR = 110;
const int FMM_ERR = 120;
// $Id$
#endif