Add datatype introspection methods to library

Adds lammps_extract_atom_datatype and lammps_extract_global_datatype functions
to allow extracting type information of properties.

python/lammps.py

@@ -40,6 +40,7 @@ LAMMPS_DOUBLE2D = 3
 LAMMPS_BIGINT = 4
 LAMMPS_TAGINT = 5
 LAMMPS_STRING = 6
+LAMMPS_TAGINT2D = 7
 
 # these must be kept in sync with the enums in library.h
 LMP_STYLE_GLOBAL = 0

src/atom.cpp

@@ -30,6 +30,7 @@
 #include "neighbor.h"
 #include "update.h"
 #include "variable.h"
+#include "library.h"
 
 #include <algorithm>
 #include <cstring>
@@ -2580,6 +2581,80 @@ void *Atom::extract(const char *name)
   return nullptr;
 }
 
+
+/** Provide data type about internal data of the Atom class
+ *
+ * \param  name  string with the keyword of the desired property.
+ * \return       data type constant for desired property or -1 */
+int Atom::extract_datatype(const char *name)
+{
+  // --------------------------------------------------------------------
+  // 5th customization section: customize by adding new variable name
+
+  if (strcmp(name,"mass") == 0) return LAMMPS_DOUBLE;
+
+  if (strcmp(name,"id") == 0) return LAMMPS_TAGINT;
+  if (strcmp(name,"type") == 0) return LAMMPS_INT;
+  if (strcmp(name,"mask") == 0) return LAMMPS_INT;
+  if (strcmp(name,"image") == 0) return LAMMPS_TAGINT;
+  if (strcmp(name,"x") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"v") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"f") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"molecule") == 0) return LAMMPS_TAGINT;
+  if (strcmp(name,"q") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"mu") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"omega") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"angmom") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"torque") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"radius") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"rmass") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"ellipsoid") == 0) return LAMMPS_INT;
+  if (strcmp(name,"line") == 0) return LAMMPS_INT;
+  if (strcmp(name,"tri") == 0) return LAMMPS_INT;
+  if (strcmp(name,"body") == 0) return LAMMPS_INT;
+
+  if (strcmp(name,"vfrac") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"s0") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"x0") == 0) return LAMMPS_DOUBLE2D;
+
+  if (strcmp(name,"spin") == 0) return LAMMPS_INT;
+  if (strcmp(name,"eradius") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"ervel") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"erforce") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"ervelforce") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"cs") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"csforce") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"vforce") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name,"etag") == 0) return LAMMPS_INT;
+
+  if (strcmp(name,"rho") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"drho") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"esph") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"desph") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"cv") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"vest") == 0) return LAMMPS_DOUBLE2D;
+
+  // USER-MESONT package
+  if (strcmp(name,"length") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"buckling") == 0) return LAMMPS_INT;
+  if (strcmp(name,"bond_nt") == 0) return  LAMMPS_TAGINT2D;
+
+  if (strcmp(name, "contact_radius") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name, "smd_data_9") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name, "smd_stress") == 0) return LAMMPS_DOUBLE2D;
+  if (strcmp(name, "eff_plastic_strain") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name, "eff_plastic_strain_rate") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name, "damage") == 0) return LAMMPS_DOUBLE;
+
+  if (strcmp(name,"dpdTheta") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"edpd_temp") == 0) return LAMMPS_DOUBLE;
+
+  // end of customization section
+  // --------------------------------------------------------------------
+
+  return -1;
+}
+
 /* ----------------------------------------------------------------------
    return # of bytes of allocated memory
    call to avec tallies per-atom vectors

src/atom.h

@@ -335,6 +335,7 @@ class Atom : protected Pointers {
   virtual void sync_modify(ExecutionSpace, unsigned int, unsigned int) {}
 
   void *extract(const char *);
+  int extract_datatype(const char *);
 
   inline int* get_map_array() {return map_array;};
   inline int get_map_size() {return map_tag_max+1;};

src/library.cpp

@@ -1206,6 +1206,98 @@ void *lammps_extract_atom(void *handle, const char *name)
 
 /* ---------------------------------------------------------------------- */
 
+/** Get data type of internal global LAMMPS variables or arrays.
+ *
+ * TODO
+ *
+ * \param  handle   pointer to a previously created LAMMPS instance
+ * \param  name     string with the name of the extracted property
+ * \return          integer constant encoding the data type of the property
+                    or -1 if not found. */
+
+int lammps_extract_global_datatype(void *handle, const char *name)
+{
+  LAMMPS *lmp = (LAMMPS *) handle;
+
+  if (strcmp(name,"units") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"dt") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"ntimestep") == 0) return LAMMPS_BIGINT;
+  if (strcmp(name,"boxlo") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"boxhi") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"boxxlo") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"boxxhi") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"boxylo") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"boxyhi") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"boxzlo") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"boxzhi") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"periodicity") == 0) return LAMMPS_INT;
+  if (strcmp(name,"triclinic") == 0) return LAMMPS_INT;
+  if (strcmp(name,"xy") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"xz") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"yz") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"natoms") == 0) return LAMMPS_BIGINT;
+  if (strcmp(name,"nbonds") == 0) return LAMMPS_BIGINT;
+  if (strcmp(name,"nangles") == 0) return LAMMPS_BIGINT;
+  if (strcmp(name,"ndihedrals") == 0) return LAMMPS_BIGINT;
+  if (strcmp(name,"nimpropers") == 0) return LAMMPS_BIGINT;
+  if (strcmp(name,"nlocal") == 0) return LAMMPS_INT;
+  if (strcmp(name,"nghost") == 0) return LAMMPS_INT;
+  if (strcmp(name,"nmax") == 0) return LAMMPS_INT;
+  if (strcmp(name,"ntypes") == 0) return LAMMPS_INT;
+
+  if (strcmp(name,"q_flag") == 0) return LAMMPS_INT;
+
+  // update->atime can be referenced as a pointer
+  // thermo "timer" data cannot be, since it is computed on request
+  // lammps_get_thermo() can access all thermo keywords by value
+
+  if (strcmp(name,"atime") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"atimestep") == 0) return LAMMPS_BIGINT;
+
+  // global constants defined by units
+
+  if (strcmp(name,"boltz") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"hplanck") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"mvv2e") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"ftm2v") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"mv2d") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"nktv2p") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"qqr2e") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"qe2f") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"vxmu2f") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"xxt2kmu") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"dielectric") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"qqrd2e") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"e_mass") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"hhmrr2e") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"mvh2r") == 0) return LAMMPS_DOUBLE;
+
+  if (strcmp(name,"angstrom") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"femtosecond") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"qelectron") == 0) return LAMMPS_DOUBLE;
+
+  return -1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+/** Get data type of a LAMMPS per-atom property
+ *
+ * TODO
+ *
+ * \param  handle  pointer to a previously created LAMMPS instance
+ * \param  name    string with the name of the extracted property
+ * \return         integer constant encoding the data type of the property
+ *                 or -1 if not found. */
+
+int lammps_extract_atom_datatype(void *handle, const char *name)
+{
+  LAMMPS *lmp = (LAMMPS *) handle;
+  return lmp->atom->extract_datatype(name);
+}
+
+/* ---------------------------------------------------------------------- */
+
 /** Create N atoms from list of coordinates
  *
 \verbatim embed:rst

src/library.h

@@ -40,6 +40,21 @@
 #include <inttypes.h>  /* for int64_t */
 #endif
 
+/** Data type constants for extracting data from atoms, computes and fixes
+ *
+ * Must be kept in sync with the equivalent constants in lammps.py */
+
+enum _LMP_DATATYPE_CONST {
+  LAMMPS_INT    = 0,
+  LAMMPS_INT2D  = 1,
+  LAMMPS_DOUBLE = 2,
+  LAMMPS_DOUBLE2D = 3,
+  LAMMPS_BIGINT = 4,
+  LAMMPS_TAGINT = 5,
+  LAMMPS_STRING = 6,
+  LAMMPS_TAGINT2D = 7
+};
+
 /** Style constants for extracting data from computes and fixes.
  *
  * Must be kept in sync with the equivalent constants in lammps.py */
@@ -113,6 +128,9 @@ int    lammps_extract_setting(void *handle, const char *keyword);
 void  *lammps_extract_global(void *handle, const char *name);
 void  *lammps_extract_atom(void *handle, const char *name);
 
+int lammps_extract_global_datatype(void *handle, const char *name);
+int lammps_extract_atom_datatype(void *handle, const char *name);
+
 #if !defined(LAMMPS_BIGBIG)
 int    lammps_create_atoms(void *handle, int n, int *id, int *type,
                            double *x, double *v, int *image, int bexpand);

unittest/c-library/test_library_properties.cpp

@@ -251,4 +251,90 @@ TEST_F(LibraryProperties, global)
     EXPECT_EQ((*b_ptr), 2);
     d_ptr = (double *)lammps_extract_global(lmp, "dt");
     EXPECT_DOUBLE_EQ((*d_ptr), 0.1);
+    int dtype = lammps_extract_global_datatype(lmp, "dt");
+    EXPECT_EQ(dtype, LAMMPS_DOUBLE);
 };
+
+class AtomProperties : public ::testing::Test {
+protected:
+    void *lmp;
+
+    AtomProperties(){};
+    ~AtomProperties() override{};
+
+    void SetUp() override
+    {
+        const char *args[] = {"LAMMPS_test", "-log",      "none",
+                              "-echo",       "screen",    "-nocite"};
+
+        char **argv = (char **)args;
+        int argc    = sizeof(args) / sizeof(char *);
+
+        ::testing::internal::CaptureStdout();
+        lmp                = lammps_open_no_mpi(argc, argv, NULL);
+        std::string output = ::testing::internal::GetCapturedStdout();
+        if (verbose) std::cout << output;
+        EXPECT_THAT(output, StartsWith("LAMMPS ("));
+        ::testing::internal::CaptureStdout();
+        lammps_command(lmp, "region box block 0 2 0 2 0 2");
+        lammps_command(lmp, "create_box 1 box");
+        lammps_command(lmp, "mass 1 3.0");
+        lammps_command(lmp, "create_atoms 1 single 1.0 1.0 1.5");
+        lammps_command(lmp, "create_atoms 1 single 0.2 0.1 0.1");
+        output = ::testing::internal::GetCapturedStdout();
+        if (verbose) std::cout << output;
+    }
+    void TearDown() override
+    {
+        ::testing::internal::CaptureStdout();
+        lammps_close(lmp);
+        std::string output = ::testing::internal::GetCapturedStdout();
+        EXPECT_THAT(output, HasSubstr("Total wall time:"));
+        if (verbose) std::cout << output;
+        lmp = nullptr;
+    }
+};
+
+TEST_F(AtomProperties, invalid)
+{
+    ASSERT_EQ(lammps_extract_atom(lmp, "UNKNOWN"), nullptr);
+}
+
+TEST_F(AtomProperties, mass)
+{
+    EXPECT_EQ(lammps_extract_atom_datatype(lmp, "mass"), LAMMPS_DOUBLE);
+    double * mass = (double *)lammps_extract_atom(lmp, "mass");
+    ASSERT_NE(mass, nullptr);
+    ASSERT_DOUBLE_EQ(mass[1], 3.0);
+}
+
+TEST_F(AtomProperties, id)
+{
+    EXPECT_EQ(lammps_extract_atom_datatype(lmp, "id"), LAMMPS_TAGINT);
+    LAMMPS_NS::tagint * id = (LAMMPS_NS::tagint *)lammps_extract_atom(lmp, "id");
+    ASSERT_NE(id, nullptr);
+    ASSERT_EQ(id[0], 1);
+    ASSERT_EQ(id[1], 2);
+}
+
+TEST_F(AtomProperties, type)
+{
+    EXPECT_EQ(lammps_extract_atom_datatype(lmp, "type"), LAMMPS_INT);
+    int * type = (LAMMPS_NS::tagint *)lammps_extract_atom(lmp, "type");
+    ASSERT_NE(type, nullptr);
+    ASSERT_EQ(type[0], 1);
+    ASSERT_EQ(type[1], 1);
+}
+
+TEST_F(AtomProperties, position)
+{
+    EXPECT_EQ(lammps_extract_atom_datatype(lmp, "x"), LAMMPS_DOUBLE2D);
+    double ** x = (double **)lammps_extract_atom(lmp, "x");
+    ASSERT_NE(x, nullptr);
+    EXPECT_DOUBLE_EQ(x[0][0], 1.0);
+    EXPECT_DOUBLE_EQ(x[0][1], 1.0);
+    EXPECT_DOUBLE_EQ(x[0][2], 1.5);
+    EXPECT_DOUBLE_EQ(x[1][0], 0.2);
+    EXPECT_DOUBLE_EQ(x[1][1], 0.1);
+    EXPECT_DOUBLE_EQ(x[1][2], 0.1);
+}