Create KIM_LAMMPS_PlugIn.h & related changes

lib/kim/Install.py

@@ -21,7 +21,7 @@ Syntax from lib dir: python Install.py -b -v version  -a kim-name
 specify one or more options, order does not matter
 
   -v = version of KIM API library to use
-       default = kim-api-v1.9.4 (current as of Mar 2018)
+       default = kim-api-v1.9.4 (current as of Apr 2018)
   -b = download and build base KIM API library with example Models
        this will delete any previous installation in the current folder
   -n = do NOT download and build base KIM API library.
@@ -166,9 +166,6 @@ if pathflag:
     mkfile.write("print_dir:\n")
     mkfile.write("	@printf $(KIM_INSTALL_DIR)\n")
 
-  with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
-    cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
-
   print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir,kimdir))
 else:
   kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version)
@@ -191,9 +188,6 @@ if buildflag:
     mkfile.write("print_dir:\n")
     mkfile.write("	@printf $(KIM_INSTALL_DIR)\n")
 
-  with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
-    cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
-
   print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir,kimdir))
 
   # download entire kim-api tarball
@@ -247,8 +241,9 @@ if buildflag:
 # add single OpenKIM model
 if addflag:
 
-  if os.path.isfile(os.path.join(thisdir, "Makefile.KIM_DIR")):
-    cmd = 'make -f Makefile.KIM_DIR print_dir'
+  makefile_path = os.path.join(thisdir, "Makefile.KIM_DIR")
+  if os.path.isfile(makefile_path):
+    cmd = 'make --no-print-directory -f %s print_dir' % makefile_path
     kimdir = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
 
   if not os.path.isdir(kimdir):

lib/kim/KIM_LAMMPS_PlugIn.h

+// Copyright 2018 Regents of the University of Minnesota
+// All rights reserved.
+//
+// Contributing authors: Ryan S. Elliott
+
+#define KIM_STATUS_OK 1
+#define KIM_STATUS_NEIGH_ITER_PAST_END 2
+#define KIM_STATUS_NEIGH_ITER_INIT_OK 3
+#define KIM_STATUS_NEIGH_INVALID_REQUEST -11
+#define KIM_STATUS_NEIGH_INVALID_MODE -6
+#define KIM_COMPUTE_FALSE 0
+#define KIM_COMPUTE_TRUE 1
+#define KIM_STATUS_FAIL 0
+
+#include "dlfcn.h"
+#include "error.h"
+
+namespace LAMMPS_NS {
+
+class KIM_LAMMPS_PlugIn {
+ public:
+  ~KIM_LAMMPS_PlugIn() {};
+  KIM_LAMMPS_PlugIn() : library(NULL) {};
+
+  bool setup_kim_api_library(Error * const error);
+  bool is_strictly_between_1_5_and_2_0;
+
+  // KIM symbols
+  void* library;
+  int (*report_error)(int line, const char *, const char *, int);
+  void (*setm_compute_by_index)(void *, int *, ...);
+  int (*model_compute)(void *);
+  int (*model_init)(void *);
+  int (*model_reinit)(void *);
+  void * (*get_sim_buffer)(void *, int *);
+  void * (*get_data_by_index)(void *, int, int *);
+  int (*model_destroy)(void *);
+  void (*free)(void *, int *);
+  int (*string_init)(void *, const char *, const char *);
+  int (*is_half_neighbors)(void *, int *);
+  int (*get_NBC_method)(void *, const char **);
+  int (*get_index)(void *, const char *, int *);
+  int (*getm_index)(void *, int *, int, ...);
+  int (*get_species_code)(void *, const char *, int *);
+  void (*setm_data_by_index)(void *, int *, int, ...);
+  int (*set_method_by_index)(void *, int, intptr_t, void (*)());
+  void (*set_sim_buffer)(void *, void *, int *);
+  int (*set_data_by_index)(void *, int, intptr_t, void *);
+  void (*set_compute_by_index)(void *, int, int, int*);
+  int (*get_num_params)(void *, int *, int *);
+  int (*get_free_parameter)(void *, const int, const char **);
+  void * (*get_data)(void *, const char *, int *);
+  intptr_t (*get_rank)(void *, const char *, int *);
+  intptr_t (*get_shape)(void *, const char *, int *, int *);
+  int (*model_info)(void *, const char *);
+};
+
+
+bool KIM_LAMMPS_PlugIn::setup_kim_api_library(Error * error)
+{
+  if (library == NULL)
+  {
+#ifdef KIM_INSTALL_DIR
+    library = dlopen(KIM_INSTALL_DIR "/lib/libkim-api-v1.so", RTLD_NOW);
+#endif
+
+    if (library == NULL)
+      library = dlopen("kim-api-v1.so", RTLD_NOW);
+
+    if (library == NULL)
+    {
+      error->all(FLERR,"KIM API library cannot be found");
+      return false;
+    }
+    else
+    {
+      // check for version and set is_strictly_between_1_5_and_2_0
+      void * ver = dlsym(library, "KIM_API_get_version");
+      if (ver == NULL)
+        is_strictly_between_1_5_and_2_0 = false;
+      else
+        is_strictly_between_1_5_and_2_0 = true;
+
+      std::string error_prefix("KIM API library error: ");
+      // get symbols
+      if (NULL == (report_error =
+                   (int (*)(int, const char *, const char *, int))
+                   dlsym(library, "KIM_API_report_error")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (setm_compute_by_index =
+                   (void (*)(void *, int *, ...))
+                   dlsym(library, "KIM_API_setm_compute_by_index")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (model_compute = (int (*)(void *))
+                   dlsym(library, "KIM_API_model_compute")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (model_init = (int (*)(void *))
+                   dlsym(library, "KIM_API_model_init")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (model_reinit = (int (*)(void *))
+                   dlsym(library, "KIM_API_model_reinit")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_sim_buffer = (void * (*)(void *, int *))
+                   dlsym(library, "KIM_API_get_sim_buffer")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_data_by_index = (void * (*)(void *, int, int *))
+                   dlsym(library, "KIM_API_get_data_by_index")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (model_destroy = (int (*)(void *))
+                   dlsym(library, "KIM_API_model_destroy")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (free = (void (*)(void *, int *))
+                   dlsym(library, "KIM_API_free")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (string_init =
+                   (int (*)(void *, const char *, const char *))
+                   dlsym(library, "KIM_API_string_init")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (is_half_neighbors = (int (*)(void *, int *))
+                   dlsym(library, "KIM_API_is_half_neighbors")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_NBC_method = (int (*)(void *, const char **))
+                   dlsym(library, "KIM_API_get_NBC_method")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_index = (int (*)(void *, const char *, int *))
+                   dlsym(library, "KIM_API_get_index")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (getm_index = (int (*)(void *, int *, int, ...))
+                   dlsym(library, "KIM_API_getm_index")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_species_code =
+                   (int (*)(void *, const char *, int *))
+                   dlsym(library, "KIM_API_get_species_code")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (setm_data_by_index =
+                   (void (*)(void *, int *, int, ...))
+                   dlsym(library, "KIM_API_setm_data_by_index")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (set_method_by_index =
+                   (int (*)(void *, int, intptr_t, void (*)()))
+                   dlsym(library, "KIM_API_set_method_by_index")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (set_sim_buffer = (void (*)(void *, void *, int *))
+                   dlsym(library, "KIM_API_set_sim_buffer")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (set_data_by_index =
+                   (int (*)(void *, int, intptr_t, void *))
+                   dlsym(library, "KIM_API_set_data_by_index")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (set_compute_by_index =
+                   (void (*)(void *, int, int, int*))
+                   dlsym(library, "KIM_API_set_compute_by_index")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_num_params = (int (*)(void *, int *, int *))
+                   dlsym(library, "KIM_API_get_num_params")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_free_parameter =
+                   (int (*)(void *, const int, const char **))
+                   dlsym(library, "KIM_API_get_free_parameter")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_data = (void * (*)(void *, const char *, int *))
+                   dlsym(library, "KIM_API_get_data")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_rank =
+                   (intptr_t (*)(void *, const char *, int *))
+                   dlsym(library, "KIM_API_get_rank")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (get_shape =
+                   (intptr_t (*)(void *, const char *, int *, int *))
+                   dlsym(library, "KIM_API_get_shape")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+      if (NULL == (model_info = (int (*)(void *, const char *))
+                   dlsym(library, "KIM_API_model_info")))
+        error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
+
+    return true;
+    }
+  }
+  else
+  {
+    return true;
+  }
+}
+
+}  // namespace LAMMPS_NS

lib/kim/Makefile.lammps

@@ -18,6 +18,6 @@
 
 include ../../lib/kim/Makefile.KIM_DIR
 
-kim_SYSINC  = -DKIM_INSTALL_DIR=\"${KIM_INSTALL_DIR}\"
-kim_SYSLIB  =
+kim_SYSINC  = -I../../lib/kim -DKIM_INSTALL_DIR=\"$(KIM_INSTALL_DIR)\"
+kim_SYSLIB  = -ldl
 kim_SYSPATH =

lib/kim/README

@@ -20,11 +20,11 @@ Instructions:
 
 1. Configure lammps for use with the kim-api library installed in this directory
 
-$ printf "KIM_INSTALL_DIR=${PWD}\n" > ./Makefile.KIM_DIR
+# replace X.Y.Z as appropriate here and below
+$ printf "KIM_INSTALL_DIR=${PWD}/installed-kim-api-vX.Y.Z\n" > ./Makefile.KIM_DIR
 
 2. Download and unpack the kim-api
 
-# replace X.Y.Z as appropriate here and below
 $ wget http://s3.openkim.org/kim-api/kim-api-vX.Y.Z.txz
 $ tar zxvf kim-api-vX.Y.Z.txz
 
@@ -36,6 +36,7 @@ $ ./configure --prefix=${PWD}/../installed-kim-api-vX.Y.Z
 
 $ make
 $ make install
+$ cd ..
 
 4. Remove source and build files
 
@@ -45,7 +46,7 @@ $ rm -rf kim-api-vX.Y.Z.txz
 5. To add items do the following (replace the kim item name with your
    desired value)
 
-$ source ${PWD}/../kim-api-vX.Y.Z/bin/kim-api-v1-activate
+$ source ${PWD}/kim-api-vX.Y.Z/bin/kim-api-v1-activate
 $ kim-api-v1-collections-management install system Pair_Johnson_Fe__MO_857282754307_002
 
 
@@ -60,4 +61,4 @@ $ make g++ (or whatever target you wish)
 
 Note that the Makefile.lammps and Makefile.KIM_DIR files in this directory
 are required to allow the LAMMPS build to find the necessary KIM files.
-You should not normally need to edit this file.
+You should not normally need to edit these files.

lib/kim/pair-kim.release.info

-This package (pair-kim-v1.7.2+1) created from commit
-
-ced1275c5fd5b382cb9bd39e44ed1324c7c85e99
-
-of the pair-kim git repository
-By Ryan S. Elliott (relliott@umn.edu) on Mon Feb 22 14:59:53 CST 2016.

src/KIM/pair_kim.h

@@ -31,12 +31,11 @@ PairStyle(kim,PairKIM)
 #ifndef LMP_PAIR_KIM_H
 #define LMP_PAIR_KIM_H
 
-// includes from KIM & LAMMPS
-//class KIM_API_model;
 #include "pair.h"
 
-
 namespace LAMMPS_NS {
+   // Forward declare KIM_LAMMPS_PlugIn
+   class KIM_LAMMPS_PlugIn;
 
    class PairKIM : public Pair {
    public:
@@ -87,6 +86,7 @@ namespace LAMMPS_NS {
       unit_sys lmps_units;
 
       // values set in set_kim_model_has_flags(), called by kim_init()
+      KIM_LAMMPS_PlugIn * kim;
       void * pkim;
       bool kim_model_has_energy;
       bool kim_model_has_forces;
@@ -145,40 +145,10 @@ namespace LAMMPS_NS {
       void set_kim_model_has_flags();
       void write_descriptor(char** test_descriptor_string);
       // static methods used as callbacks from KIM
+      static void * (*kim_get_sim_buffer)(void *, int *);
       static int get_neigh(void** kimmdl, int* mode, int* request,
                            int* atom, int* numnei, int** nei1atom,
                            double** pRij);
-
-     bool setup_kim_api_library();
-     static bool kim_api_is_strictly_between_1_5_and_2_0;
-     // KIM symbols
-     static void* kim_api_library;
-     static int (*report_error)(int line, const char *, const char *, int);
-     static void (*kim_api_setm_compute_by_index)(void *, int *, ...);
-     static int (*kim_api_model_compute)(void *);
-     static int (*kim_api_model_init)(void *);
-     static int (*kim_api_model_reinit)(void *);
-     static void * (*kim_api_get_sim_buffer)(void *, int *);
-     static void * (*kim_api_get_data_by_index)(void *, int, int *);
-     static int (*kim_api_model_destroy)(void *);
-     static void (*kim_api_free)(void *, int *);
-     static int (*kim_api_string_init)(void *, const char *, const char *);
-     static int (*kim_api_is_half_neighbors)(void *, int *);
-     static int (*kim_api_get_NBC_method)(void *, const char **);
-     static int (*kim_api_get_index)(void *, const char *, int *);
-     static int (*kim_api_getm_index)(void *, int *, int, ...);
-     static int (*kim_api_get_species_code)(void *, const char *, int *);
-     static void (*kim_api_setm_data_by_index)(void *, int *, int, ...);
-     static int (*kim_api_set_method_by_index)(void *, int, intptr_t, void (*)());
-     static void (*kim_api_set_sim_buffer)(void *, void *, int *);
-     static int (*kim_api_set_data_by_index)(void *, int, intptr_t, void *);
-     static void (*kim_api_set_compute_by_index)(void *, int, int, int*);
-     static int (*kim_api_get_num_params)(void *, int *, int *);
-     static int (*kim_api_get_free_parameter)(void *, const int, const char **);
-     static void * (*kim_api_get_data)(void *, const char *, int *);
-     static intptr_t (*kim_api_get_rank)(void *, const char *, int *);
-     static intptr_t (*kim_api_get_shape)(void *, const char *, int *, int *);
-     static int (*kim_api_model_info)(void *, const char *);
    };
 }