Merge pull request #4088 from sakibmatin/debug

Fix for force calculation and memory bug (atom name definition) in mliap.

src/KOKKOS/mliap_unified_couple_kokkos.pyx

@@ -13,6 +13,7 @@ from libc.stdint cimport uintptr_t
 cimport cython
 from cpython.ref cimport PyObject
 from libc.stdlib cimport malloc, free
+from libc.string cimport memcpy
 
 
 cdef extern from "lammps.h" namespace "LAMMPS_NS":
@@ -451,15 +452,24 @@ cdef public object mliap_unified_connect_kokkos(char *fname, MLIAPDummyModel * m
 
     cdef int nelements = <int>len(unified.element_types)
     cdef char **elements = <char**>malloc(nelements * sizeof(char*))
+    cdef char * c_str
+    cdef char * s
+    cdef ssize_t slen
 
     if not elements:
         raise MemoryError("failed to allocate memory for element names")
 
-    cdef char *elem_name
     for i, elem in enumerate(unified.element_types):
-        elem_name_bytes = elem.encode('UTF-8')
+        py_str = elem.encode('UTF-8')
-        elem_name = elem_name_bytes
+        s = py_str
-        elements[i] = &elem_name[0]
+        slen = len(py_str)
+        c_str = <char *>malloc((slen+1)*sizeof(char))
+        if not c_str:
+            raise MemoryError("failed to allocate memory for element names")
+        memcpy(c_str, s, slen)
+        c_str[slen] = 0
+        elements[i] = c_str
+
     unified_int.descriptor.set_elements(elements, nelements)
     unified_int.model.nelements = nelements
 

src/KOKKOS/mliap_unified_kokkos.cpp

@@ -315,7 +315,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij)
     int i = pair_i[ii];
     int j = j_atoms[ii];
     // must not count any contribution where i is not a local atom
-    if (i < nlocal) {
       Kokkos::atomic_add(&f[i*3+0], fij[ii3+0]);
       Kokkos::atomic_add(&f[i*3+1], fij[ii3+1]);
       Kokkos::atomic_add(&f[i*3+2], fij[ii3+2]);
@@ -352,7 +351,6 @@ void LAMMPS_NS::update_pair_forces(MLIAPDataKokkosDevice *data, double *fij)
           Kokkos::atomic_add(&d_vatom(j,3), 0.5*v[3]);
           Kokkos::atomic_add(&d_vatom(j,4), 0.5*v[4]);
           Kokkos::atomic_add(&d_vatom(j,5), 0.5*v[5]);
-        }
       }
     }
   });
@@ -382,11 +380,9 @@ void LAMMPS_NS::update_atom_energy(MLIAPDataKokkosDevice *data, double *ei)
 
   Kokkos::parallel_reduce(nlocal, KOKKOS_LAMBDA(int i, double &local_sum){
     double e = ei[i];
-    // must not count any contribution where i is not a local atom
+    
-    if (i < nlocal) {
+    d_eatoms[i] = e;
-      d_eatoms[i] = e;
+    local_sum += e;
-      local_sum += e;
-    }
   },*data->energy);
 }
 

src/ML-IAP/mliap_unified.cpp

@@ -254,10 +254,8 @@ void LAMMPS_NS::update_pair_energy(MLIAPData *data, double *eij)
     double e = 0.5 * eij[ii];
 
     // must not count any contribution where i is not a local atom
-    if (i < nlocal) {
+    data->eatoms[i] += e;
-      data->eatoms[i] += e;
+    e_total += e;
-      e_total += e;
-    }
   }
   data->energy = e_total;
 }
@@ -277,17 +275,14 @@ void LAMMPS_NS::update_pair_forces(MLIAPData *data, double *fij)
     int i = data->pair_i[ii];
     int j = data->jatoms[ii];
 
-    // must not count any contribution where i is not a local atom
+    f[i][0] += fij[ii3];
-    if (i < nlocal) {
+    f[i][1] += fij[ii3 + 1];
-      f[i][0] += fij[ii3];
+    f[i][2] += fij[ii3 + 2];
-      f[i][1] += fij[ii3 + 1];
+    f[j][0] -= fij[ii3];
-      f[i][2] += fij[ii3 + 2];
+    f[j][1] -= fij[ii3 + 1];
-      f[j][0] -= fij[ii3];
+    f[j][2] -= fij[ii3 + 2];
-      f[j][1] -= fij[ii3 + 1];
-      f[j][2] -= fij[ii3 + 2];
 
-      if (data->vflag) data->pairmliap->v_tally(i, j, &fij[ii3], data->rij[ii]);
+    if (data->vflag) data->pairmliap->v_tally(i, j, &fij[ii3], data->rij[ii]);
-    }
   }
 }
 

src/ML-IAP/mliap_unified_couple.pyx

@@ -8,6 +8,7 @@ import lammps.mliap
 cimport cython
 from cpython.ref cimport PyObject
 from libc.stdlib cimport malloc, free
+from libc.string cimport memcpy
 
 
 cdef extern from "lammps.h" namespace "LAMMPS_NS":
@@ -387,15 +388,26 @@ cdef public object mliap_unified_connect(char *fname, MLIAPDummyModel * model,
 
     cdef int nelements = <int>len(unified.element_types)
     cdef char **elements = <char**>malloc(nelements * sizeof(char*))
+    cdef char * c_str
+    cdef char * s
+    cdef ssize_t slen
 
     if not elements:
         raise MemoryError("failed to allocate memory for element names")
 
-    cdef char *elem_name
     for i, elem in enumerate(unified.element_types):
-        elem_name_bytes = elem.encode('UTF-8')
+        py_str = elem.encode('UTF-8')
-        elem_name = elem_name_bytes
+
-        elements[i] = &elem_name[0]
+        s = py_str
+        slen = len(py_str)
+        c_str = <char *>malloc((slen+1)*sizeof(char))
+        if not c_str:
+            raise MemoryError("failed to allocate memory for element names")
+        memcpy(c_str, s, slen)
+        c_str[slen] = 0
+        
+        elements[i] = c_str
+    
     unified_int.descriptor.set_elements(elements, nelements)
     unified_int.model.nelements = nelements