Added a few files to begin translating
This commit is contained in:
Adam Parler
parent
c0f6f4d1c4
commit
7e8da872a1
6 changed files with 2910 additions and 0 deletions
64
src/basis/getlibr.py
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64
src/basis/getlibr.py
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#!/usr/bin/env python3
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# This script downloads the basis set library data from www.basissetexchange.org
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# into the directory $NWCHEM_TOP/src/basis/libraries.bse
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# to use, set the env. variable NWCHEM_BASIS_LIBRARY=$NWCHEM_TOP/src/basis/libraries.bse/
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# Requires the installation of the python env. from
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# https://github.com/MolSSI-BSE/basis_set_exchange
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# See https://molssi-bse.github.io/basis_set_exchange/
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#
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# names changed
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# def2-universal-jfit was weigend_coulomb_fitting
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# dgauss-a1-dftjfit was dgauss_a1_dft_coulomb_fitting
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# dgauss-a2-dftjfit was dgauss_a2_dft_coulomb_fitting
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#
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import basis_set_exchange as bse
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from datetime import datetime
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today = datetime.now().isoformat(timespec='minutes')
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print(today)
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all_bs = bse.get_all_basis_names()
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md = bse.get_metadata()
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for bas_name in all_bs:
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#get version and list of elements
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version_bs = md[bas_name]['latest_version']
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elements_list = md[bas_name]['versions'][version_bs]['elements']
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#open file
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# get rid of asterisks
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file_name = bas_name.replace("*","s")
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#get rid of parenthesis
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file_name = file_name.replace("(","")
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file_name = file_name.replace(")","")
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#replace commas with underscore
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file_name = file_name.replace(",","_")
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#replace whitespace with underscore
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file_name = file_name.replace(" ","_")
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#replace forward slash with underscore
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file_name = file_name.replace("/","_")
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print(' file name is '+file_name+"\n")
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output_file = open(file_name,'w')
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output_file.write('# BSE Version '+bse.version()+'\n')
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output_file.write('# Data downloaded at '+today+'\n')
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output_file.write('# '+bas_name+' version number '+version_bs+'\n')
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output_file.write('# Description: '+md[bas_name]['description']+'\n')
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output_file.write('# Role: '+md[bas_name]['role']+'\n')
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output_file.write('# '+bse.get_references(bas_name,fmt='txt').replace('\n','\n# '))
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output_file.write('# \n')
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for element in elements_list:
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#element='h'
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try:
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bs_str=bse.get_basis(bas_name, header=False, elements=element, fmt='nwchem', optimize_general=True, uncontract_general=True)
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except:
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# print("failed for"+element)
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pass
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else:
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bs_str=bs_str.replace("BASIS","basis")
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bs_str=bs_str.replace("END","end")
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bs_str=bs_str.replace("PRINT","")
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element_str=bse.misc.compact_elements([element])
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bs_str=bs_str.replace("ao basis",element_str+"_"+bas_name)
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#ECP
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bs_str=bs_str.replace("ECP","ecp \""+element_str+"_"+bas_name+"\"")
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output_file.write(bs_str)
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#
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print(bas_name+" "+element_str)
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print("end")
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403
src/nwchem.cpp
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403
src/nwchem.cpp
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#include <stdint.h>
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#include <stdio.h>
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#include "errquit.h"
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#include "rtdb.h"
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#ifdef USE_TCGMSG
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#include "tcgmsg.h"
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#else
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int NODEID;
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extern NODEID;
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#endif
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#include "pstat.h"
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#include "util.h"
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#include "inp.h"
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#include "bgj_common.h"
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#include "stdio.h"
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int RTDB;
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int STACK;
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int HEAP;
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int GLOBAL;
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bool STATUS;
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bool OVERIFY, OHARDFAIL;
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#ifdef CRAY_T3D
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int oldact, fsigctl;
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#endif
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#ifdef PSCALE
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int IO_CODE;
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#else
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int32_t IO_CODE;
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#endif
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// $Id$
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// ======================================================================================================
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//> \mainpage Northwest Computational Chemistry Package (NWChem) 7.0.2
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//>
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//> NWChem is an open-source computational chemistry package distributed under the terms of
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//> the Educational Community License (ECL) 2.0
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//>
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//> This software and its documentation were developed at the EMSL at Pacific Northwest National Laboratory,
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//> a multiprogram national laboratory, operated for the U.S. Department of Energy by Battelle under
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//> Contract Number DE-AC05-76RL01830. Support for this work was provided by the Department of Energy
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//> Office of Biological and Environmental Research, Office of Basic Energy Science, and the Office of
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//> Advanced Scientific Computing.
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//>
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//> Licensed under the Educational Community License, Version 2.0 (the "License"); you may
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//> not use this file except in compliance with the License. You may obtain a copy of the
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//> License at <a href="https://opensource.org/licenses/ECL-2.0">https://opensource.org/licenses/ECL-2.0</a>.
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//>
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//> Unless required by applicable law or agreed to in writing, software distributed under the
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//> License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
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//> either express or implied. See the License for the specific language governing
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//> permissions and limitations under the License.
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//>
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//> Further information, including user documentation and forums, may be found at
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//> <a href="http://www.nwchem-sw.org/">http://www.nwchem-sw.org/</a>. Alternatively,
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//> the paper
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//>
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//> * M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. Van Dam,
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//> D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong (2010)<br>
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//> "NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations"<br>
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//> <I>Computer Physics Communications</I>, <b>181</b>, 1477–1489, DOI: <a href="https://doi.org/10.1016/j.cpc.2010.04.018">10.1016/j.cpc.2010.04.018</a>
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//>
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//> provides details on the codes capabilities.
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//>
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//> Copyright (c) 1994-2020 Pacific Northwest National Laboratory, Battelle Memorial Institute
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//>
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//> Environmental Molecular Sciences Laboratory (EMSL)<br>
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//> Pacific Northwest National Laboratory<br>
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//> Richland, WA 99352
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// ======================================================================================================
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int main(){
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char input_filename[nw_max_path_len], rtdb_name[nw_max_path_len];
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double total_wall, total_cpu;
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#ifdef USE_OFFLOAD
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int ppnout;
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bool offload_enabled;
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extern offload_enabled;
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int offload_device;
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extern offload_device;
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#endif
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bool ostartup, ocontinue, orestart;
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bool input_parse;
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extern input_parse;
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#if defined(USE_OPENMP)
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int omp_get_max_threads;
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extern omp_get_max_threads;
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#endif
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// Create parallel processes and initialize IPC layer
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pbeginf();
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// MXINIT is needed by PeIGS and PFFT to initialize
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// the communication fabric they use.
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mxinit();
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// Initialize timers so they are relative to job start
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total_wall = -util_wallsec();
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total_cpu = -util_cpusec();
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// Only process 0 opens the input file
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// (note that ga_nodeid() does not work yet!)
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if (nodeid() == 0){
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// Get the name of the input file from the command line
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get_input_filename(input_filename);
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try {
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FILE * LuIn = fopen(input_filename,'r');
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}
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catch {
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errquit('nwchem: failed to open the input file', 0, INPUT_ERR);
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}
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}
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else{
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#if !(defined(KSR) || defined(IBM) || defined(FUJITSU_SOLARIS) ||defined(FUJITSU_VPP) ||defined(FUJITSU_VPP64))
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fclose(LuIn);
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#endif
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}
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// Look for memory directive in the input ... must eventually
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// open the rtdb first so that can get memory directive out of that
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// if it is not in the input
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// The user input model has well-defined categories of memory,
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// each of which has a specific size. How we use these limits
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// depends on the platform we are running on.
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input_mem_size(stack, heap, global, overify, ohardfail);
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// Initialize local memory allocator & global array tools
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ga_initialize_ltd(ma_sizeof(mt_dbl,global,mt_byte));
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// this must happen after GA and before MA
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util_setup_gpu_affinity();
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if ( ga_uses_ma() ) {
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if (!ma_init(mt_dbl, stack, heap+global)){
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errquit('nwchem.F: ma_init failed (ga_uses_ma=T)',911, MA_ERR);
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}
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} else{
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if (!ma_init(mt_dbl,stack,heap)) {
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errquit('nwchem.F: ma_init failed (ga_uses_ma=F)',911, MA_ERR);
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}
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}
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// Touch OpenMP here so that any runtime initialization happens up-front.
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// This ensures that any printout that the OpenMP runtime generates,
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// such as affinity information, appears at the top of the output file.
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// Otherwise, it might not appear until e.g. the CCSD module, at which
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// point it will pollute the output file in an undesirable way.
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// Do not move this in front of GA/MPI/TCGMSG initialization, since the
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// OpenMP runtime may inherit affinity information from MPI that is only
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// determined during MPI initialization.
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// Format definition is outside of preprocessor protection to ensure the
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// label is not accidentally reused, since that will not be caught by
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// testing that does not enable OpenMP.
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g99 format(2x, 'NWChem w/ OpenMP: Maximum threads = ',i4);
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#if defined(USE_OPENMP){
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#pragma omp parallel
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#pragma omp master
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{
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if (ga_nodeid() == 0){
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write(luout,g99);
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omp_get_max_threads();
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}
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}
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#endif
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// set no. threads for threaded BLAS to 1
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util_blas_set_num_threads(1);
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rtdb_init()
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// More for amusement then efficiency force all MA allocated entities
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// to be aligned at the beginning of a 128 byte cache line
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// if (!ma_set_numalign(7)){
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// errquit('nwchem.cpp: ma_set_numalign failed',911, MA_ERR);
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// }
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// aligned to 64byte record
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if (!ma_set_numalign(6)){
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errquit('nwchem.cpp: ma_set_numalign failed', 911, MA_ERR);
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}
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//old:------------------------------------------------------- START ---------
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//old:C GA allocations come out of MA space, so lump them together
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//old:C and let MA impose the limits on GA sizes instead of actually
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//old:C using the global limit.
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//old:C
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//old: if ( ga_uses_ma() ) then
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//old: if (.not. ma_init(mt_dbl, stack, heap+global))
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//old: $ call errquit('nwchem: ma_init failed', -1)
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//old: call ga_initialize
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//old:C
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//old:C GA allocations are separate from MA, so the separate limit
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//old:C must be enforced. Note GA only understands bytes.
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//old:C
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//old: else
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//old: if (.not. ma_init(mt_dbl, stack, heap))
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//old: $ call errquit('nwchem: ma_init failed', -1)
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//old: call ga_initialize_ltd(ma_sizeof(mt_dbl, global, mt_byte) )
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//old: endif
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//old:------------------------------------------------------- END -----------
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//*** call nxtval_ga_initialize()
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// Trap SIGFPE after GA to override handler
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//*** call ieeetrap()
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#if defined(LINUXALPHA)
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dec_fpe(); // To avoid underflow problems on Alpha in Texas
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#endif
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#ifdef CRAY_T3D
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// This as a temporary fix for SIGFPE in Texas that does not seem
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// to affect the final results
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oldact = fsigctl('IGNORE','SIGFPE',0);
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#endif
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#ifdef LINUX
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// uncommenting this line turns on sigfpe trapping under linux
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// linux_trapfpe();
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#endif
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#ifdef MACX
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// uncommenting this line turns on sigfpe trapping under Mac OSX
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// macx_trapfpe();
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#endif
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// Hard fail is good for development but means that we cannot
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// respond to allocation problems. Disable by default.
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status = ma_set_auto_verify(overify);
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status = ma_set_hard_fail(ohardfail);
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status = ma_set_error_print(ohardfail);
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// Initialize pstat
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if (!pstat_init(20,1,' ')){
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errquit('nwchem: pstat_init failed', 0, UNKNOWN_ERR);
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}
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input_file_info(input_filename, rtdb_name, ostartup, ocontinue);
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// Now are ready to summarize the environment
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nwchem_banner(input_filename, rtdb_name, ostartup, ocontinue);
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// Actually open the database and store the file prefix
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// Note that only process 0 has the database name ... that is OK.
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if (ostartup){
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if (!rtdb_open(rtdb_name, 'empty', rtdb)){
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errquit('start: rtdb_open empty failed', 0, RTDB_ERR);
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}
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} else{
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if (!rtdb_open(rtdb_name, 'old', rtdb)){
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errquit('start: rtdb_open old failed', 0, RTDB_ERR);
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}
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}
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// initialize nxtask
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nxtask_init(rtdb);
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//!! BGJ
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bgj_rtdb = rtdb;
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//!! BGJ
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if (ostartup || ocontinue){
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orestart = false;
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} else{
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orestart = true;
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}
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util_set_rtdb_state(rtdb, ostartup, ocontinue, orestart);
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util_file_info_rtdb(rtdb); // Save file info for restart
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movecs_ecce_print_on();
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geom_hnd_parallel(true)
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perfm_start();
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#ifdef USE_OFFLOAD
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util_getppn(ppnout);
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if (ppnout == 0){
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errquit('util_getppn failed',0,UERR);
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}
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if (ga_nodeid() == 0){
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write(luout,*) ga_nodeid(), ' ppn ', ppnout;
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}
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if (offload_enabled()){
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if (ga_nodeid() < ppnout){
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write(luout, '(I8,A,I2)') ga_nodeid(), ' offload enabled, GPU: ',
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offload_device();
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}
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}
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ga_sync()
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#endif
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if (orestart || ocontinue){
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nw_print_restart_info(rtdb);
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}
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// if continue then go right to task stored on rtdb do not further parse
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// input. if input is required then user should have used restart
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if (ocontinue){
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task(rtdb);
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}
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// Parse input data, shove into database and execute tasks
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g10 if (input_parse(rtdb)){ // while(tasks to do)
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util_print_rtdb_load(rtdb, ' '); // High level print
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if (util_print('tcgmsg', print_never)){
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setdbg(1);
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} else{
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setdbg(0);
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}
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#ifdef CATAMOUNT
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util_allocga();
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#endif
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task(rtdb);
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goto g10; // end while
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}
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// Close the RTDB
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util_print_rtdb_load(rtdb, ' '); // High level print
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if (util_print('rtdbvalues', print_debug)){
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if (!rtdb_print(rtdb,true)){
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errquit('control: rtdb_print failed', 0, RTDB_ERR);
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}
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} else if (util_print('rtdb', print_high)){
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if (! rtdb_print(rtdb, false)){
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errquit('control: rtdb_print failed', 0, RTDB_ERR);
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}
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}
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if (!rtdb_close(rtdb, 'keep')){
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errquit('nwchem: rtdb_close failed', rtdb, RTDB_ERR);
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}
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if (util_print('rtdb', print_high) || util_print('rtdbvalues', print_high)){
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rtdb_print_usage(); // Called after closing so memory leaks apparent
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}
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// Tidy up pstat
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if (!pstat_terminate()){
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errquit('nwchem: pstat_terminate failed', 0, UNKNOWN_ERR);
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}
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//** nxtval_ga_terminate()
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// Print memory and other info
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ga_sync();
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if (ga_nodeid == 0){
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if (util_print('ga summary', print_default)){
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ga_summarize(0);
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}
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if (util_print('ga stats', print_default)){
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ga_print_stats();
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write(LuOut,*);
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}
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}
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return 0;
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}
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105
src/rtdb/rtdb.h
Normal file
105
src/rtdb/rtdb.h
Normal file
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@ -0,0 +1,105 @@
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//
|
||||
// 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;
|
||||
2273
src/tce/oce.py
Normal file
2273
src/tce/oce.py
Normal file
File diff suppressed because it is too large
Load diff
32
src/tce/splitfiles.py
Normal file
32
src/tce/splitfiles.py
Normal file
|
|
@ -0,0 +1,32 @@
|
|||
#!/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()
|
||||
|
||||
if (not source):
|
||||
print("Usage: python splitfiles.py < inputfile.F")
|
||||
|
||||
nfiles = 0
|
||||
for line in source:
|
||||
if (string.find(line,"SUBROUTINE") != -1):
|
||||
if (nfiles):
|
||||
file = open(filename+".F","w")
|
||||
for newline in filecontent:
|
||||
file.write(newline)
|
||||
filename = string.split(line[string.find(line,"SUBROUTINE")+11:],"(")[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")
|
||||
for newline in filecontent:
|
||||
file.write(newline)
|
||||
print("Number of files generated:",nfiles)
|
||||
33
src/util/errquit.h
Normal file
33
src/util/errquit.h
Normal file
|
|
@ -0,0 +1,33 @@
|
|||
// UERR - Not yet assigned to a category
|
||||
// UNKNOWN_ERR - Not yet assigned to a category
|
||||
// MEM_ERROR - 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
|
||||
// BASIS_ERR - Error related to basis set
|
||||
// GEOM_ERR - Error related to geometry
|
||||
// MA_ERR - local memory error
|
||||
// GA_ERR - global memory error
|
||||
// INT_ERR - error related to integrals
|
||||
// DISK_ERR - error in reading or writing from disk
|
||||
// CALC_ERR - calculation failed to converge
|
||||
// FMM_ERR -
|
||||
// STACK_ERR - error in MA stack
|
||||
// HEAP_ERR - error in MA heap
|
||||
const int UERR = 0;
|
||||
const int UNKNOWN_ERR = 0;
|
||||
const int MEM_ERR = 10;
|
||||
const int STACK_ERR = 11;
|
||||
const int HEAP_ERR = 12;
|
||||
const int RTDB_ERR = 20;
|
||||
const int INPUT_ERR = 30;
|
||||
const int CAPMIS_ERR = 40;
|
||||
const int BASIS_ERR = 50;
|
||||
const int GEOM_ERR = 60;
|
||||
const int GA_ERR = 70;
|
||||
const int MA_ERR = 80;
|
||||
const int INT_ERR = 90;
|
||||
const int DISK_ERR = 100;
|
||||
const int CALC_ERR = 110;
|
||||
const int FMM_ERR = 120;
|
||||
// $Id$
|
||||
Loading…
Add table
Add a link
Reference in a new issue