Merge pull request #3278 from yury-lysogorskiy/feature/ml-pace-multispecies

ML_PACE package hybrid support and small updates

cmake/Modules/LAMMPSUtils.cmake

@@ -24,6 +24,24 @@ function(validate_option name values)
     endif()
 endfunction(validate_option)
 
+# helper function for getting the most recently modified file or folder from a glob pattern
+function(get_newest_file path variable)
+  file(GLOB _dirs ${path})
+  set(_besttime 2000-01-01T00:00:00)
+  set(_bestfile "<unknown>")
+  foreach(_dir ${_dirs})
+    file(TIMESTAMP ${_dir} _newtime)
+    if(_newtime IS_NEWER_THAN _besttime)
+      set(_bestfile ${_dir})
+      set(_besttime ${_newtime})
+    endif()
+  endforeach()
+  if(_bestfile STREQUAL "<unknown>")
+    message(FATAL_ERROR "Could not find valid path at: ${path}")
+  endif()
+  set(${variable} ${_bestfile} PARENT_SCOPE)
+endfunction()
+
 function(get_lammps_version version_header variable)
     file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
     set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,6 +1,6 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "e0572de57039d4afedefb25707b6ceae" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "32394d799bc282bb57696c78c456e64f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 
@@ -13,8 +13,8 @@ execute_process(
   COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
   WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
 )
+get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
 
-file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
 # enforce building libyaml-cpp as static library and turn off optional features
 set(YAML_BUILD_SHARED_LIBS OFF)
 set(YAML_CPP_BUILD_CONTRIB OFF)

lib/pace/Install.py

@@ -15,7 +15,7 @@ from install_helpers import fullpath, geturl, checkmd5sum
 # settings
 
 thisdir = fullpath('.')
-version = 'v.2021.10.25.fix'
+version = 'v.2021.10.25.fix2'
 
 # known checksums for different PACE versions. used to validate the download.
 checksums = { \
@@ -23,7 +23,8 @@ checksums = { \
         'v.2021.4.9'      : '4db54962fbd6adcf8c18d46e1798ceb5',
         'v.2021.9.28'     : 'f98363bb98adc7295ea63974738c2a1b',
         'v.2021.10.25'    : 'a2ac3315c41a1a4a5c912bcb1bc9c5cc',
-	'v.2021.10.25.fix': 'e0572de57039d4afedefb25707b6ceae'
+        'v.2021.10.25.fix': 'e0572de57039d4afedefb25707b6ceae',
+        'v.2021.10.25.fix2': '32394d799bc282bb57696c78c456e64f'
         }
 
 

src/ML-PACE/pair_pace.cpp

@@ -146,18 +146,8 @@ void PairPACE::compute(int eflag, int vflag)
   // the pointer to the list of neighbors of "i"
   firstneigh = list->firstneigh;
 
-  if (inum != nlocal) error->all(FLERR, "inum: {} nlocal: {} are different", inum, nlocal);
-
-  // Aidan Thompson told RD (26 July 2019) that practically always holds:
-  // inum = nlocal
-  // i = ilist(ii) < inum
-  // j = jlist(jj) < nall
-  // neighborlist contains neighbor atoms plus skin atoms,
-  //       skin atoms can be removed by setting skin to zero but here
-  //       they are disregarded anyway
-
   //determine the maximum number of neighbours
-  int max_jnum = -1;
+  int max_jnum = 0;
   int nei = 0;
   for (ii = 0; ii < list->inum; ii++) {
     i = ilist[ii];
@@ -190,7 +180,7 @@ void PairPACE::compute(int eflag, int vflag)
 
     try {
       aceimpl->ace->compute_atom(i, x, type, jnum, jlist);
-    } catch (exception &e) {
+    } catch (std::exception &e) {
       error->one(FLERR, e.what());
     }
 
@@ -325,10 +315,16 @@ void PairPACE::coeff(int narg, char **arg)
 
   const int n = atom->ntypes;
   for (int i = 1; i <= n; i++) {
-    char *elemname = elemtypes[i - 1];
+    char *elemname = arg[2 + i];
+    if (strcmp(elemname, "NULL") == 0) {
+      // species_type=-1 value will not reach ACE Evaluator::compute_atom,
+      // but if it will ,then error will be thrown there
+      aceimpl->ace->element_type_mapping(i) = -1;
+      map[i] = -1;
+      if (comm->me == 0) utils::logmesg(lmp, "Skipping LAMMPS atom type #{}(NULL)\n", i);
+    } else {
       int atomic_number = AtomicNumberByName_pace(elemname);
       if (atomic_number == -1) error->all(FLERR, "'{}' is not a valid element\n", elemname);
-
       SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname);
       if (mu != -1) {
         if (comm->me == 0)
@@ -342,10 +338,11 @@ void PairPACE::coeff(int narg, char **arg)
                    potential_file_name);
       }
     }
+  }
 
   // initialize scale factor
   for (int i = 1; i <= n; i++) {
-    for (int j = i; j <= n; j++) { scale[i][j] = 1.0; }
+    for (int j = i; j <= n; j++) scale[i][j] = 1.0;
   }
 
   aceimpl->ace->set_basis(*aceimpl->basis_set, 1);