src/basis/getlibr.py

@@ -0,0 +1,64 @@
+#!/usr/bin/env 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/
+# Requires the installation of the python env. from
+# https://github.com/MolSSI-BSE/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']
+    #open file
+    # get rid of asterisks
+    file_name = bas_name.replace("*","s")
+    #get rid of parenthesis
+    file_name = file_name.replace("(","")
+    file_name = file_name.replace(")","")
+    #replace commas with underscore
+    file_name = file_name.replace(",","_")
+    #replace whitespace with underscore
+    file_name = file_name.replace(" ","_")
+    #replace forward slash with underscore
+    file_name = file_name.replace("/","_")
+    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('# '+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('# '+bse.get_references(bas_name,fmt='txt').replace('\n','\n# '))
+    output_file.write('# \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)
+        except:
+#            print("failed for"+element)
+            pass
+        else:
+            bs_str=bs_str.replace("BASIS","basis")
+            bs_str=bs_str.replace("END","end")
+            bs_str=bs_str.replace("PRINT","")
+            element_str=bse.misc.compact_elements([element])
+            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")
+

src/nwchem.cpp

@@ -0,0 +1,403 @@
+#include <stdint.h>
+#include <stdio.h>
+#include "errquit.h"
+#include "rtdb.h"
+#ifdef USE_TCGMSG
+    #include "tcgmsg.h"
+#else
+    int NODEID;
+    extern NODEID;
+#endif
+#include "pstat.h"
+#include "util.h"
+#include "inp.h"
+#include "bgj_common.h"
+#include "stdio.h"
+    int RTDB;
+    int STACK;
+    int HEAP;
+    int GLOBAL;
+    bool STATUS;
+    bool OVERIFY, OHARDFAIL;
+#ifdef CRAY_T3D
+      int oldact, fsigctl;
+#endif
+#ifdef PSCALE
+    int IO_CODE;
+#else
+    int32_t IO_CODE;
+#endif
+
+//  $Id$
+
+// ======================================================================================================
+//> \mainpage Northwest Computational Chemistry Package (NWChem) 7.0.2
+//>
+//> NWChem is an open-source computational chemistry package distributed under the terms of
+//> the Educational Community License (ECL) 2.0
+//>
+//> This software and its documentation were developed at the EMSL at Pacific Northwest National Laboratory,
+//> a multiprogram national laboratory, operated for the U.S. Department of Energy by Battelle under
+//> Contract Number DE-AC05-76RL01830. Support for this work was provided by the Department of Energy
+//> Office of Biological and Environmental Research, Office of Basic Energy Science, and the Office of
+//> Advanced Scientific Computing.
+//>
+//> Licensed under the Educational Community License, Version 2.0 (the "License"); you may
+//> not use this file except in compliance with the License. You may obtain a copy of the
+//> License at <a href="https://opensource.org/licenses/ECL-2.0">https://opensource.org/licenses/ECL-2.0</a>.
+//>
+//> Unless required by applicable law or agreed to in writing, software distributed under the
+//> License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
+//> either express or implied. See the License for the specific language governing
+//> permissions and limitations under the License.
+//>
+//> Further information, including user documentation and forums, may be found at
+//> <a href="http://www.nwchem-sw.org/">http://www.nwchem-sw.org/</a>. Alternatively,
+//> the paper
+//>
+//> * M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. Van Dam,
+//>   D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong (2010)<br>
+//>   "NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations"<br>
+//>   <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>
+//>
+//> provides details on the codes capabilities.
+//>
+//> Copyright (c) 1994-2020 Pacific Northwest National Laboratory, Battelle Memorial Institute
+//>
+//> Environmental Molecular Sciences Laboratory (EMSL)<br>
+//> Pacific Northwest National Laboratory<br>
+//> Richland, WA 99352
+
+// ======================================================================================================
+
+
+int main(){
+    char input_filename[nw_max_path_len], rtdb_name[nw_max_path_len];
+    double total_wall, total_cpu;
+    #ifdef USE_OFFLOAD
+        int ppnout;
+        bool offload_enabled;
+        extern offload_enabled;
+        int offload_device;
+        extern offload_device;
+    #endif
+
+    bool ostartup, ocontinue, orestart;
+    bool input_parse;
+    extern input_parse;
+    #if defined(USE_OPENMP)
+        int omp_get_max_threads;
+        extern omp_get_max_threads;
+    #endif
+
+//    Create parallel processes and initialize IPC layer
+
+    pbeginf();
+
+//    MXINIT is needed by PeIGS and PFFT to initialize
+//    the communication fabric they use.
+
+    mxinit();
+
+//    Initialize timers so they are relative to job start
+
+    total_wall = -util_wallsec();
+    total_cpu  = -util_cpusec();
+
+//    Only process 0 opens the input file
+//    (note that ga_nodeid() does not work yet!)
+
+    if (nodeid() == 0){
+
+//    Get the name of the input file from the command line
+
+        get_input_filename(input_filename);
+
+        try {
+            FILE * LuIn = fopen(input_filename,'r');
+        }
+        catch {
+            errquit('nwchem: failed to open the input file', 0, INPUT_ERR);
+        }
+    }
+    else{
+        #if !(defined(KSR) || defined(IBM) || defined(FUJITSU_SOLARIS) ||defined(FUJITSU_VPP) ||defined(FUJITSU_VPP64))
+            fclose(LuIn);
+        #endif
+      }
+
+//    Look for memory directive in the input ... must eventually
+//    open the rtdb first so that can get memory directive out of that
+//    if it is not in the input
+
+//    The user input model has well-defined categories of memory,
+//    each of which has a specific size.  How we use these limits
+//    depends on the platform we are running on.
+
+    input_mem_size(stack, heap, global, overify, ohardfail);
+
+//    Initialize local memory allocator & global array tools
+
+    ga_initialize_ltd(ma_sizeof(mt_dbl,global,mt_byte));
+    // this must happen after GA and before MA
+    util_setup_gpu_affinity();
+    if ( ga_uses_ma() ) {
+        if (!ma_init(mt_dbl, stack, heap+global)){
+            errquit('nwchem.F: ma_init failed (ga_uses_ma=T)',911, MA_ERR);
+        }
+    } else{
+        if (!ma_init(mt_dbl,stack,heap)) {
+            errquit('nwchem.F: ma_init failed (ga_uses_ma=F)',911, MA_ERR);
+        }
+    }
+
+//    Touch OpenMP here so that any runtime initialization happens up-front.
+//    This ensures that any printout that the OpenMP runtime generates,
+//    such as affinity information, appears at the top of the output file.
+//    Otherwise, it might not appear until e.g. the CCSD module, at which
+//    point it will pollute the output file in an undesirable way.
+
+//    Do not move this in front of GA/MPI/TCGMSG initialization, since the
+//    OpenMP runtime may inherit affinity information from MPI that is only
+//    determined during MPI initialization.
+
+//    Format definition is outside of preprocessor protection to ensure the
+//    label is not accidentally reused, since that will not be caught by
+//    testing that does not enable OpenMP.
+
+    g99 format(2x, 'NWChem w/ OpenMP: Maximum threads = ',i4);
+    #if defined(USE_OPENMP){
+        #pragma omp parallel
+        #pragma omp master
+        {
+            if (ga_nodeid() == 0){
+                write(luout,g99);
+                omp_get_max_threads();
+            }
+        }
+    #endif
+//    set no. threads for threaded BLAS to 1
+    util_blas_set_num_threads(1);
+
+    rtdb_init()
+
+//    More for amusement then efficiency force all MA allocated entities
+//    to be aligned at the beginning of a 128 byte cache line
+
+//    if (!ma_set_numalign(7)){
+//        errquit('nwchem.cpp: ma_set_numalign failed',911, MA_ERR);
+//    }
+//    aligned to 64byte record
+    if (!ma_set_numalign(6)){
+        errquit('nwchem.cpp: ma_set_numalign failed', 911, MA_ERR);
+    }
+
+
+//old:------------------------------------------------------- START ---------
+//old:C     GA allocations come out of MA space, so lump them together
+//old:C     and let MA impose the limits on GA sizes instead of actually
+//old:C     using the global limit.
+//old:C
+//old:      if ( ga_uses_ma() ) then
+//old:         if (.not. ma_init(mt_dbl, stack, heap+global))
+//old:     $      call errquit('nwchem: ma_init failed', -1)
+//old:         call ga_initialize
+//old:C
+//old:C     GA allocations are separate from MA, so the separate limit
+//old:C     must be enforced.  Note GA only understands bytes.
+//old:C
+//old:      else
+//old:         if (.not. ma_init(mt_dbl, stack, heap))
+//old:     $      call errquit('nwchem: ma_init failed', -1)
+//old:         call ga_initialize_ltd(ma_sizeof(mt_dbl, global, mt_byte) )
+//old:      endif
+//old:------------------------------------------------------- END -----------
+
+//***      call nxtval_ga_initialize()
+
+//    Trap SIGFPE after GA to override handler
+
+//***      call ieeetrap()
+    #if defined(LINUXALPHA)
+          dec_fpe();  // To avoid underflow problems on Alpha in Texas
+    #endif
+    #ifdef CRAY_T3D
+    //    This as a temporary fix for SIGFPE in Texas that does not seem
+    //    to affect the final results
+        oldact = fsigctl('IGNORE','SIGFPE',0);
+    #endif
+    #ifdef LINUX
+//      uncommenting this line turns on sigfpe trapping under linux
+//      linux_trapfpe();
+    #endif
+    #ifdef MACX
+//      uncommenting this line turns on sigfpe trapping under Mac OSX
+//      macx_trapfpe();
+    #endif
+//      Hard fail is good for development but means that we cannot
+//      respond to allocation problems. Disable by default.
+    status = ma_set_auto_verify(overify);
+    status = ma_set_hard_fail(ohardfail);
+    status = ma_set_error_print(ohardfail);
+
+//      Initialize pstat
+
+    if (!pstat_init(20,1,' ')){
+        errquit('nwchem: pstat_init failed', 0, UNKNOWN_ERR);
+    }
+
+    input_file_info(input_filename, rtdb_name, ostartup, ocontinue);
+
+//    Now are ready to summarize the environment
+
+    nwchem_banner(input_filename, rtdb_name, ostartup, ocontinue);
+
+//    Actually open the database and store the file prefix
+
+//    Note that only process 0 has the database name ... that is OK.
+
+    if (ostartup){
+        if (!rtdb_open(rtdb_name, 'empty', rtdb)){
+            errquit('start: rtdb_open empty failed', 0, RTDB_ERR);
+        }
+    } else{
+        if (!rtdb_open(rtdb_name, 'old', rtdb)){
+            errquit('start: rtdb_open old failed', 0, RTDB_ERR);
+        }
+    }
+    
+
+//    initialize nxtask
+    nxtask_init(rtdb);
+
+//!! BGJ
+    bgj_rtdb = rtdb;
+//!! BGJ
+
+
+    if (ostartup || ocontinue){
+        orestart = false;
+    } else{
+        orestart = true;
+    }
+
+    util_set_rtdb_state(rtdb, ostartup, ocontinue, orestart);
+    util_file_info_rtdb(rtdb); // Save file info for restart
+    movecs_ecce_print_on();
+    geom_hnd_parallel(true)
+    perfm_start();
+
+    #ifdef USE_OFFLOAD
+        util_getppn(ppnout);
+        if (ppnout == 0){
+            errquit('util_getppn failed',0,UERR);
+        }
+        if (ga_nodeid() == 0){
+            write(luout,*) ga_nodeid(), ' ppn ', ppnout;
+        }
+        if (offload_enabled()){
+            if (ga_nodeid() < ppnout){
+                write(luout, '(I8,A,I2)') ga_nodeid(), ' offload enabled, GPU: ',
+                offload_device();
+            }
+        }
+        ga_sync()
+    #endif
+
+    if (orestart || ocontinue){
+        nw_print_restart_info(rtdb);
+    }
+
+// if continue then go right to task stored on rtdb do not further parse
+// input. if input is required then user should have used restart
+
+    if (ocontinue){
+        task(rtdb);
+    }
+
+//    Parse input data, shove into database and execute tasks
+
+    g10 if (input_parse(rtdb)){ // while(tasks to do)
+        util_print_rtdb_load(rtdb, ' '); // High level print
+        if (util_print('tcgmsg', print_never)){
+            setdbg(1);
+        } else{
+            setdbg(0);
+        }
+        #ifdef CATAMOUNT
+            util_allocga();
+        #endif
+
+        task(rtdb);
+        goto g10;            // end while
+    }
+
+//    Close the RTDB
+
+    util_print_rtdb_load(rtdb, ' '); // High level print
+    if (util_print('rtdbvalues', print_debug)){
+        if (!rtdb_print(rtdb,true)){
+            errquit('control: rtdb_print failed', 0, RTDB_ERR);
+        }
+    } else if (util_print('rtdb', print_high)){
+        if (! rtdb_print(rtdb, false)){
+            errquit('control: rtdb_print failed', 0, RTDB_ERR);
+        }
+    }
+    
+    if (!rtdb_close(rtdb, 'keep')){
+        errquit('nwchem: rtdb_close failed', rtdb, RTDB_ERR);
+    }
+
+    if (util_print('rtdb', print_high) || util_print('rtdbvalues', print_high)){
+        rtdb_print_usage();   // Called after closing so memory leaks apparent
+    }
+
+//    Tidy up pstat
+
+    if (!pstat_terminate()){
+        errquit('nwchem: pstat_terminate failed', 0, UNKNOWN_ERR);
+    }
+
+//**      nxtval_ga_terminate()
+
+//    Print memory and other info
+
+    ga_sync();
+    if (ga_nodeid == 0){
+        if (util_print('ga summary', print_default)){
+            ga_summarize(0);
+        }
+        if (util_print('ga stats', print_default)){
+            ga_print_stats();
+            write(LuOut,*);
+        }
+        
+    }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+    return 0;
+}

src/rtdb/rtdb.h

@@ -0,0 +1,105 @@
+//
+//    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;

src/tce/splitfiles.py

@@ -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)

src/util/errquit.h

@@ -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;
+// $Id$