Merge pull request #68 from RKLindsey/develop

Fix I/O bugs, update documentation, refactor LAMMPS test suite

Author: RKLindsey

.gitignore

@@ -0,0 +1 @@
+etc/lmp/tests/*/correct_output/*

chimesFF/src/FP/chimesFF.cpp

@@ -727,8 +727,9 @@ void chimesFF::read_parameters(string paramfile)
         	        }
 		}
 		else
-		{
-			cout << "chimesFF: \tType is excluded... skipping." << endl;
+		{	
+			if (rank == 0)
+				cout << "chimesFF: \tType is excluded... skipping." << endl;
 		}
             }    
 
@@ -1058,7 +1059,8 @@ void chimesFF::read_parameters(string paramfile)
 		}
 		else
 		{
-			cout << "chimesFF: \tType is excluded... skipping." << endl;		
+			if (rank == 0)
+				cout << "chimesFF: \tType is excluded... skipping." << endl;		
 		}
             }    
 
@@ -2266,7 +2268,6 @@ void chimesFF::build_pair_int_quad_map()
     // to support GPU environment without string operations.
     // This must be called prior to force evaluation.
 
-    cout << "Entered weird func" << endl;
     const int natoms = 4 ;
     const int npairs = natoms * (natoms-1) / 2 ;
     vector<int> pair_map(npairs) ;
@@ -2317,13 +2318,15 @@ void chimesFF::build_pair_int_quad_map()
         if ( pair_int_quad_map[i].size() == 0 )
         {
 		if (atom_int_quad_map[i] >= 0)
-            		cout << "Error: Did not initialize pair_int_quad_map for entry " << i << endl ;
+			if(rank==0)
+            			cout << "Error: Did not initialize pair_int_quad_map for entry " << i << endl ;
 		else
-			cout << "Warning: Did not initialize pair_int_quad_map for excluded entry " << i << endl ;
+			if(rank==0)
+				cout << "Warning: Did not initialize pair_int_quad_map for excluded entry " << i << endl ;
         }
     }   
     GlobalParams::pair_int_quad_mapping = pair_int_quad_map;
-    cout << "Assigned global param" << endl;
+    //cout << "Assigned global param" << endl;
 }
 
 void chimesFF::build_pair_int_trip_map()
@@ -2375,9 +2378,11 @@ void chimesFF::build_pair_int_trip_map()
         if ( pair_int_trip_map[i].size() == 0 )
         {
 		if (atom_int_trip_map[i] >= 0)
-            		cout << "Error: Did not initialize pair_int_trip_map for entry " << i << endl ;
+			if(rank==0)
+            			cout << "Error: Did not initialize pair_int_trip_map for entry " << i << endl ;
 		else
-			cout << "Warning: Did not initialize pair_int_trip_map for excluded entry " << i << endl ;
+			if(rank==0)
+				cout << "Warning: Did not initialize pair_int_trip_map for excluded entry " << i << endl ;
         }
     }
 

chimesFF/src/FP/histogram

@@ -22,21 +22,28 @@ int my_rank;
 #include <iomanip>
 #include "chimesFF.h"  // Make sure this includes the GlobalParams namespace declaration
 
-void print_global_params() {
+void print_global_params() 
+{
 
     // Print 2-body cutoffs
+    if (my_rank == 0)
+    {
     cout << "\n2-Body Cutoffs:\n";
-    for (size_t i = 0; i < rcut_2b_list.size(); ++i) {
+    for (size_t i = 0; i < rcut_2b_list.size(); ++i) 
+    {
         cout << "Pair " << i << ": ";
         cout << "Inner = " << fixed << setprecision(4) << rcut_2b_list[i][0];
         cout << ", Outer = " << rcut_2b_list[i][1] << "\n";
     }
+   
 
     // Print 3-body cutoffs
     cout << "\n3-Body Cutoffs:\n";
-    for (size_t i = 0; i < rcut_3b_list.size(); ++i) {
+    for (size_t i = 0; i < rcut_3b_list.size(); ++i) 
+    {
         cout << "Triplet " << i << ":\n";
-        for (size_t j = 0; j < rcut_3b_list[i].size(); ++j) {
+        for (size_t j = 0; j < rcut_3b_list[i].size(); ++j) 
+	{
             cout << "  Pair " << j << ": ";
             cout << "Inner = " << rcut_3b_list[i][j][0];
             cout << ", Outer = " << rcut_3b_list[i][j][1] << "\n";
@@ -45,9 +52,11 @@ void print_global_params() {
 
     // Print 4-body cutoffs
     cout << "\n4-Body Cutoffs:\n";
-    for (size_t i = 0; i < rcut_4b_list.size(); ++i) {
+    for (size_t i = 0; i < rcut_4b_list.size(); ++i) 
+    {
         cout << "Quadruplet " << i << ":\n";
-        for (size_t j = 0; j < rcut_4b_list[i].size(); ++j) {
+        for (size_t j = 0; j < rcut_4b_list[i].size(); ++j) 
+	{
             cout << "  Pair " << j << ": ";
             cout << "Inner = " << rcut_4b_list[i][j][0];
             cout << ", Outer = " << rcut_4b_list[i][j][1] << "\n";
@@ -56,11 +65,13 @@ void print_global_params() {
 
     // Print Morse lambda values
     cout << "\nMorse Lambda Values:\n";
-    for (size_t i = 0; i < morse_lambda_list.size(); ++i) {
+    for (size_t i = 0; i < morse_lambda_list.size(); ++i) 
+    {
         cout << "Pair " << i << ": λ = " 
                   << fixed << setprecision(4) 
                   << morse_lambda_list[i] << "\n";
     }
+    }
 }
 
 int split_lines(string line, vector<string> & items)
@@ -569,7 +580,8 @@ int main(int argc, char *argv[])
         vector<double> f1_2b_atom_types, f2_2b_atom_types;
         int npairs_2b = 1;
         read_flat_clusters(f1_2b, npairs_2b, f1_2b_flat_clusters, f1_2b_atom_types, 2);
-        cout << "Read in 2B clusters..." << endl;
+        if (my_rank == 0)	
+		cout << "Read in 2B clusters..." << endl;
         read_flat_clusters(f2_2b, npairs_2b, f2_2b_flat_clusters, f2_2b_atom_types, 2);
 
         // Process 3B clusters
@@ -579,7 +591,8 @@ int main(int argc, char *argv[])
         vector<double> f1_3b_atom_types, f2_3b_atom_types;
         int npairs_3b = 3;
         read_flat_clusters(f1_3b, npairs_3b, f1_3b_flat_clusters, f1_3b_atom_types, 3);
-        cout << "Read in 3B clusters..." << endl;
+        if (my_rank == 0)
+		cout << "Read in 3B clusters..." << endl;
         read_flat_clusters(f2_3b, npairs_3b, f2_3b_flat_clusters, f2_3b_atom_types, 3);
 
         // Process 4B clusters
@@ -589,7 +602,8 @@ int main(int argc, char *argv[])
         vector<double> f1_4b_atom_types, f2_4b_atom_types; 
         int npairs_4b = 6;
         read_flat_clusters(f1_4b, npairs_4b, f1_4b_flat_clusters, f1_4b_atom_types, 4);
-        cout << "Read in 4B clusters..." << endl;
+        if (my_rank == 0)
+		cout << "Read in 4B clusters..." << endl;
         read_flat_clusters(f2_4b, npairs_4b, f2_4b_flat_clusters, f2_4b_atom_types, 4);
 
         if (my_rank == 0) {
@@ -612,4 +626,4 @@ int main(int argc, char *argv[])
 
     MPI_Finalize();
     return 0;
-}
+}

chimesFF/src/FP/multi_calc_histogram.cpp

@@ -36,7 +36,7 @@ for body in 2b 3b 4b; do
                     sub(/_clusters\.txt$/, "_list.txt", list_file); 
                     print cluster_file; 
                     print list_file
-                }' "$framefile" | xargs rm -v
+                }' "$framefile" | xargs rm -v > /dev/null 2>&1 
             else
                 echo "  Error concatenating files, preserving originals"
             fi
@@ -48,4 +48,4 @@ for body in 2b 3b 4b; do
 done
 
 echo -e "\nCombination complete. Created files:"
-ls -l *b_combined.txt
+ls -l *-clusters.txt | awk '{print $NF}'

chimesFF/src/FP/post_process.sh

@@ -938,9 +938,10 @@ void chimesFF::read_parameters(string paramfile)
         	        }
 		}
 		else if (tmp_str_items[4] == "EXCLUDED:")
-        {
-            cout << "chimesFF: \tType is excluded... skipping." << endl;
-        }
+        	{
+		if (rank == 0)
+            		cout << "chimesFF: \tType is excluded... skipping." << endl;
+        	}
             }   
 
             if(line.find("TRIPMAPS:") != string::npos)
@@ -1269,7 +1270,8 @@ void chimesFF::read_parameters(string paramfile)
 		}
 		else
 		{
-			cout << "chimesFF: \tType is excluded... skipping." << endl;		
+			if (rank == 0)
+				cout << "chimesFF: \tType is excluded... skipping." << endl;		
 		}
             }    
 
@@ -3009,9 +3011,11 @@ void chimesFF::build_pair_int_quad_map()
         if ( pair_int_quad_map[i].size() == 0 )
         {
 		if (atom_int_quad_map[i] >= 0)
-            		cout << "Error: Did not initialize pair_int_quad_map for entry " << i << endl ;
+			if(rank==0)
+            			cout << "Error: Did not initialize pair_int_quad_map for entry " << i << endl ;
 		else
-			cout << "Warning: Did not initialize pair_int_quad_map for excluded entry " << i << endl ;
+			if(rank==0)
+				cout << "Warning: Did not initialize pair_int_quad_map for excluded entry " << i << endl ;
         }
     }   
 }
@@ -3065,9 +3069,11 @@ void chimesFF::build_pair_int_trip_map()
         if ( pair_int_trip_map[i].size() == 0 )
         {
 		if (atom_int_trip_map[i] >= 0)
-            		cout << "Error: Did not initialize pair_int_trip_map for entry " << i << endl ;
+			if(rank==0)
+            			cout << "Error: Did not initialize pair_int_trip_map for entry " << i << endl ;
 		else
-			cout << "Warning: Did not initialize pair_int_trip_map for excluded entry " << i << endl ;
+			if(rank==0)
+				cout << "Warning: Did not initialize pair_int_trip_map for excluded entry " << i << endl ;
         }
     }
 

chimesFF/src/chimesFF.cpp

@@ -1,64 +1,49 @@
-.. _page-etc:
 
-Support for Linking with External Codes
-=============================================
+.. _etc:
 
-Using the ChIMES Calculator with LAMMPS
-******************************************
+ChIMES in LAMMPS
+=============================================
 
-We are currently working toward ChIMES calculator implementation in `LAMMPS <https://lammps.sandia.gov>`_ as a USER package. In the interim, the following provides a guide to implementing the ChIMES calculator as a LAMMPS pairstyle.
+We are currently working toward ChIMES calculator implementation in `LAMMPS <https://lammps.sandia.gov>`_ as a USER package. In the interim, we have provided a capability for compiling the `stable_29Aug2024_update1 <https://github.com/lammps/lammps.git build/>`_ version of LAMMPS with ChIMES as a pairstyle in this package.
 
 
 
 Quick start
 ^^^^^^^^^^^^^^^^
 
-Provided a system with a C++11-compatible compiler and an MPI compatible compiler are available, LAMMPS can be downloaded, installed, linked to ChIMES, and compiled all at once by navigating to ``etc/lmp``, adding Intel compilers to your path  and executing ``./install.sh``. Once complete, the installation can be tested by navigating to ``etc/lmp/tests`` and running the example via ``../exe/lmp_mpi_chimes -i in.lammps``. 
+.. Note ::
 
-As with installation of the ChIMES Calculator itself, if you are on a HPC using module files, you may need to load them first. Module files are already configured for a handful of HPC - inspect the contents of modfiles to see if
-yours is listed. If it is (e.g., LLNL-LC.mod), execute ``export hosttype=LLNL-LC; ./install.sh`` to install. Otherwise, load the appropriate modules by hand before running the
-install script.
+    To compile LAMMPS with ChIMES, you must have C++11 and MPI compilers avillable. As with installation of the ChIMES Calculator itself, if you are on a HPC using module files, you may need to load them first. Module files are already configured for a handful of HPC - inspect the contents of modfiles to see if yours is listed. If it is (e.g., LLNL-LC.mod), execute ``export hosttype=LLNL-LC`` Otherwise, load the appropriate modules by hand before running the install script.
 
-Note that Intel oneapi compilers (which are now free) can be used to properly configure your enviroment for all Intel capabilities (e.g., icc, mpiicpc, mkl, etc.) - simply locate and execute the setvars.sh script within your Intel installation.
+    Note that Intel oneapi compilers (which are now free) can be used to properly configure your enviroment for all Intel capabilities (e.g., icc, mpiicpc, mkl, etc.) - simply locate and execute the setvars.sh script within your Intel installation.
 
 
------
 
-Detailed Compilation Overview
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Navigate to ``etc/lmp`` and execute  ``./install.sh`` to install. Once complete, the installation can be tested by navigating to ``etc/lmp/tests`` and either running the entire test suite via ``./run_tests.sh``, which takes roughly 15 minutes, or running an individual test by entering an example folder and executing ``../../exe/lmp_mpi_chimes -i in.lammps``. 
 
+The install script compiles with LAMMPS packages ``manybody`` and ``extra-pair``. Additional packages can be included by adding appropriate commands to the ``etc/lmp/install.sh`` script. For example, to add the MOLECULE package, one would add the line highlighted in yellow below:
 
-.. Note::
 
-    This example assumes users have downloaded the 29 Oct 2020 release of LAMMPS (stable version as of 10/29/20), which can be downloaded `here <https://lammps.sandia.gov/download.html>`_. 
+.. code-block :: 
+    :lineno-start: 114
+    :emphasize-lines: 6
     
+    # Compile
     
-
-To integrate the ChIMES calculator in LAMMPS, locate the following files, and place them in the following destination among the LAMMPS source code:
-
-========================    ================    ================    ==============
-File                        Location            Destination         Description
-========================    ================    ================    ==============
-``chimesFF.{h,cpp}``        ``chimesFF/src``    ``src/MANYBODY``    ChIMES calculator files
-``pair_chimes.{h,cpp}``     ``etc/lmp/src``     ``src/MANYBODY``    ChIMES pair_style definition files
-``pair.{h,cpp}``            ``etc/lmp/etc``     ``src``             Updated LAMMPS pair files (new ev_tally definition added)
-``Makefile.mpi_chimes``     ``etc/lmp/etc``     ``src/MAKE``        Makefile for compiling with ChIMES support
-========================    ================    ================    ==============
-
-
-Following, compile from the base LAMMPS directory with:
-
-.. code-block:: shell
-
+    cd build/${lammps}/src
     make yes-manybody
-    make mpi_chimes
+    make yes-extra-pair
+    make yes-molecule
+    make -j 4 mpi_chimes
+    cd -
 
-Note that a successful compilation should produce an executable named ``lmp_mpi_chimes``.
+    
 
-.. Tip::
 
-        If you are using an intel compiler, either delete the ``pair_list.*`` files that appear in the src folder following the ``make yes-manybody`` command, or add ``-restrict`` to ``CCFLAGS`` in ``MAKE/Makefile.mpi_chimes``. Note that the presently provided ``Makefile.mpi_chimes`` utilizes the latter approach.
+.. Tip ::
 
+    Additional flags can be specified during installation to enable features such as model tabulation and configuration fingerprint generation. For more details, see the :ref:`utils` page.
+    
 
 Running
 ^^^^^^^^^^^^^^^^