Merge pull request #7 from ZimmermanGroup:joshkamm/issue5

Joshkamm/issue5

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.github/pull_request_template.md

@@ -0,0 +1,8 @@
+- [ ] Implement changes
+- [ ] Update documentation
+- [ ] Update tests
+- [ ] Look through pull request changes
+- [ ] Clean up code and retest
+- [ ] Increment version number
+
+Closes ISSUE

.github/workflows/ci.yml

@@ -0,0 +1,15 @@
+# This workflow will compile ZStruct including dependencies
+name: CI
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up pixi
+      uses: prefix-dev/setup-pixi@v0.8.1
+    - name: Compile and test
+      run: pixi run start

.gitignore

@@ -0,0 +1,13 @@
+# C++ build files
+*.o
+*.exe
+
+# output from testing the tutorial
+# a copy of the output is version controlled under tutorial/example
+tutorial/scratch
+tutorial/DUPLICATES
+tutorial/GSMDATA*
+
+# pixi environments
+.pixi
+*.egg-info

Makefile

@@ -3,22 +3,19 @@
 # Executable name
 CMD = zstruct.exe
 
-# -------- description of DFLAGS ---------------
-
 
-# -------- Define environmental variable C_COMPILER -----------
-# Make sure it is defined
-#          ifeq ($(strip$(FORTRAN_COMPILER)),)
-# Otherwise you can define it here also by uncommenting next line
- FC = icpc -openmp -I$(MKLROOT)/include
+ FC = icpx -I"${CONDA_PREFIX}/include"
+#  FC = icpc -qopenmp -I$(MKLROOT)/include
 # FC = g++ -fopenmp -I$(MKLROOT)/include
+
+# -------- description of DFLAGS ---------------
 DFLAGS =  #-Define the cpp flags to be used
-#DFLAGS =  #-Define the cpp flags to be used
 OFLAGS =  # optimization
 
-#Intel parallel openmp (only w/icpc compiler)
+# Intel parallel openmp (only w/ intel compiler?)
+# generated using https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-link-line-advisor.html
+LINKERFLAGS =  -L${CONDA_PREFIX}/lib -lmkl_intel_ilp64 -lmkl_tbb_thread -lmkl_core -lpthread -lm -ldl 
 #LINKERFLAGS =  -L$(MKLROOT)/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm
-LINKERFLAGS =  -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread 
 # MAC OS linkers
 #LINKERFLAGS = -lm -framework Accelerate
 

README.md

@@ -3,10 +3,20 @@ code for ZStruct-2
 
 ## Overview
 
-ZStruct is a package for automated reaction discovery developed in c++.
+ZStruct is a package for automated reaction discovery developed in C++.
 
-For more information, check out the wiki page: https://github.com/ZimmermanGroup/ZStruct/wiki
+For more information, check out the wiki page (somewhat out of date but hopefully still useful): https://github.com/ZimmermanGroup/ZStruct/wiki
 
 Sample tutorial files can be found under the tutorial folder: https://github.com/ZimmermanGroup/ZStruct/tree/master/tutorial
 
 ## Installation
+
+First, clone this github repository.
+
+Aug 2024: Attempting a more reproducible build with [Pixi](https://pixi.sh), a tool built on the conda ecosystem to manage both dependencies and configuration / installation workflows.
+
+The pixi.toml file in this repository specifies the dependency package names as they appear on [conda-forge](https://conda-forge.org/) and installation tasks. You can use pixi (simple installation instructions [here](https://pixi.sh)) to install the dependencies and execute the build, or reference the configuration files and do something equivalent using your preferred tools.
+
+With pixi, I built ZStruct by navigating into the ZStruct git repository and executing `pixi run start` which installs the dependencies, executes the Makefile, and if successful runs the built executable.
+
+Notes: The build has succeeded in a github actions environment which is a freshly cloned linux virtual machine. On our computing cluster, I find that I either need to unload one of our default linux modules or clear the LD_LIBRARY_PATH with `export LD_LIBRARY_PATH=""`. I assume this avoids a conflicting version of some dependency taking priority over the version installed for ZStruct.

icoord.cpp

@@ -1458,7 +1458,7 @@ void ICoord::structure_read(string xyzfile)
 
   string line;
   bool success=true;
-  success=getline(infile, line);
+  success=(bool)getline(infile, line);
   if (success)
   {
     int length=StringTools::cleanstring(line);
@@ -1469,7 +1469,7 @@ void ICoord::structure_read(string xyzfile)
   printf("   natoms: %2i natomsa: %2i \n",natoms,natomsa);
   if (natoms<1) { printf(" ERROR: natoms must be > 0 \n"); exit(1); }
 
-  success=getline(infile, line);
+  success=(bool)getline(infile, line);
   if (success) comment = line;
 
   anumbers = new int[1+natomsa];
@@ -1478,7 +1478,7 @@ void ICoord::structure_read(string xyzfile)
 
   //cout <<"  -Reading the atomic names...";
   for (int i=0;i<natoms;i++){
-    success=getline(infile, line);
+    success=(bool)getline(infile, line);
     int length=StringTools::cleanstring(line);
     vector<string> tok_line = StringTools::tokenize(line, " \t");
     anames[i] = tok_line[0];
@@ -1502,10 +1502,10 @@ void ICoord::structure_read(string xyzfile)
   fflush(stdout);
 
 
-  success=getline(infile, line);
-  success=getline(infile, line);
+  success=(bool)getline(infile, line);
+  success=(bool)getline(infile, line);
   for (int j=0;j<natoms;j++){
-    success=getline(infile, line);
+    success=(bool)getline(infile, line);
     int length=StringTools::cleanstring(line);
     vector<string> tok_line = StringTools::tokenize(line, " \t");
     coords[3*j+0]=atof(tok_line[1].c_str());

nbo.cpp

@@ -622,7 +622,7 @@ int NBO::read_mopac_mo(string filename)
   int offset = 0;
   while(!infile.eof())
   {
-    success = getline(infile,line);
+    success = (bool)getline(infile,line);
     if (line.find("NO. OF FILLED LEVELS")!=string::npos)
     {
       tok_line = StringTools::tokenize(line, " \t");
@@ -640,9 +640,9 @@ int NBO::read_mopac_mo(string filename)
     {
      // printf(" found ROOT NO, cao: %2i \n",cao);
       //cout << " RR1: " << line << endl;
-      success = getline(infile,line);
+      success = (bool)getline(infile,line);
       //cout << " RR2: " << line << endl;
-      success = getline(infile,line);
+      success = (bool)getline(infile,line);
       //cout << " RR3: " << line << endl;
       tok_line = StringTools::tokenize(line, " \t");
 
@@ -653,15 +653,15 @@ int NBO::read_mopac_mo(string filename)
       for (int i=0;i<nnew;i++)
         mo_occ[offset+i] = atof(tok_line[i].c_str());
 
-      success = getline(infile,line);
+      success = (bool)getline(infile,line);
       //cout << " RR4: " << line << endl;
-      success = getline(infile,line);
+      success = (bool)getline(infile,line);
       //cout << " RR5: " << line << endl;
 
       //starting here, MO coefs
       for (int i=0;i<natoms;i++)
       {
-        success = getline(infile,line);
+        success = (bool)getline(infile,line);
         //cout << " RRat: " << line << endl;
         tok_line = StringTools::tokenize(line, " \t");
         nnew = tok_line.size() - 3;
@@ -673,7 +673,7 @@ int NBO::read_mopac_mo(string filename)
           for (int j=0;j<nnew;j++)
             MO[(offset+j)*nao+cao] = atof(tok_line[3+j].c_str());
           cao += 1;
-          success = getline(infile,line);
+          success = (bool)getline(infile,line);
         }
         else if (tok_line[1]=="B" || tok_line[1]=="C" || tok_line[1]=="N" || tok_line[1]=="O" || tok_line[1]=="F")
         {
@@ -685,7 +685,7 @@ int NBO::read_mopac_mo(string filename)
             for (int j=0;j<nnew;j++)
               MO[(offset+j)*nao+cao] = atof(tok_line[3+j].c_str());
             cao += 1;
-            success = getline(infile,line);
+            success = (bool)getline(infile,line);
           }
         }
       }
@@ -717,14 +717,14 @@ int NBO::read_mopac_mo(string filename)
   int nhp = 0;
   while (!infile.eof())
   {
-    success = getline(infile,line);
+    success = (bool)getline(infile,line);
     if (line.find("NET ATOMIC CHARGES")!=string::npos)
     {
-      success = getline(infile,line);
-      success = getline(infile,line);
+      success = (bool)getline(infile,line);
+      success = (bool)getline(infile,line);
       for (int i=0;i<natoms;i++)
       {
-        success = getline(infile,line);
+        success = (bool)getline(infile,line);
        // cout << " RR1: " << line << endl;
         tok_line = StringTools::tokenize(line, " \t");
         q[i] = atof(tok_line[2].c_str());
@@ -739,11 +739,11 @@ int NBO::read_mopac_mo(string filename)
     }
     if (line.find("NUMBER OF CENTERS")!=string::npos)
     {
-      success = getline(infile,line);
-      success = getline(infile,line);
+      success = (bool)getline(infile,line);
+      success = (bool)getline(infile,line);
       while (!infile.eof())
       {
-        success = getline(infile,line);
+        success = (bool)getline(infile,line);
         tok_line = StringTools::tokenize(line, " \t");
         int lsize = tok_line.size();
         if (lsize>0)
@@ -899,7 +899,7 @@ int NBO::read_mo(string filename)
   mheadersize = 0;
   while(!infile.eof())
   {
-    success = getline(infile,line);
+    success = (bool)getline(infile,line);
     if (line.find("[MO]")!=string::npos)
       break;
     if (mcounting)
@@ -915,7 +915,7 @@ int NBO::read_mo(string filename)
   infile.open(filename.c_str());
   while(!infile.eof())
   {
-    success = getline(infile,line);
+    success = (bool)getline(infile,line);
     if (line.find("[Molden Format]")!=string::npos)
       mcounting = 1;
     if (mcounting)
@@ -931,13 +931,13 @@ int NBO::read_mo(string filename)
   infile.open(filename.c_str());
   while(!infile.eof())
   {
-    success = getline(infile,line);
+    success = (bool)getline(infile,line);
     if (line.find("[GTO]")!=string::npos)
     {
      // cout << " RR00: " << line << endl;
       while(line.find("[MO]")==string::npos)
       {
-        success = getline(infile,line);
+        success = (bool)getline(infile,line);
        // cout << " RR0: " << line << endl;
         tok_line = StringTools::tokenize(line, " \t");
         if (tok_line.size()>1)
@@ -948,7 +948,7 @@ int NBO::read_mo(string filename)
             int cont = 1;
             while(cont)
             {
-              success = getline(infile,line);
+              success = (bool)getline(infile,line);
               tok_line = StringTools::tokenize(line, " \t");
               //cout << "  RR0: " << line << endl;
               if (line.find("S")!=string::npos)
@@ -988,15 +988,15 @@ int NBO::read_mo(string filename)
     }
   }
   for (int i=0;i<4;i++)
-    success = getline(infile,line);
+    success = (bool)getline(infile,line);
 
   printf("  found %i ao's (with 3p 5d etc) \n",nao);
 
   double* jMO1 = new double[MAX_BASIS]; //Note max basis limit
   int dim = 0;
   while (!infile.eof())
   {
-    success = getline(infile,line);
+    success = (bool)getline(infile,line);
     if (line.find("Sym")!=string::npos)
     {
       //cout << " RR1: " << line << endl;
@@ -1021,13 +1021,13 @@ int NBO::read_mo(string filename)
   nmo = 1;
   while (!infile.eof())
   {
-    success = getline(infile,line);
+    success = (bool)getline(infile,line);
     cout << " RRX: " << line << endl;
     if (line.find("Occup=")!=string::npos)
     {
       for (int j=0;j<nao;j++)
       {
-        success = getline(infile,line);
+        success = (bool)getline(infile,line);
         cout << " RRY: " << line << endl;
         tok_line = StringTools::tokenize(line, " \t");
         MO[nmo*nao+j] = atof(tok_line[1].c_str());