From 3f3bab4e7199833f50123abe1777edaf90e369ee Mon Sep 17 00:00:00 2001
From: "Ryan S. Elliott" <relliott@umn.edu>
Date: Mon, 2 Apr 2018 09:38:30 -0500
Subject: [PATCH] Create KIM_LAMMPS_PlugIn.h & related changes
---
lib/kim/Install.py | 13 +-
lib/kim/KIM_LAMMPS_PlugIn.h | 210 ++++++++++++++++++++++
lib/kim/Makefile.lammps | 4 +-
lib/kim/README | 9 +-
lib/kim/pair-kim.release.info | 6 -
src/KIM/pair_kim.cpp | 326 ++++++++--------------------------
src/KIM/pair_kim.h | 38 +---
7 files changed, 295 insertions(+), 311 deletions(-)
create mode 100644 lib/kim/KIM_LAMMPS_PlugIn.h
delete mode 100644 lib/kim/pair-kim.release.info
diff --git a/lib/kim/Install.py b/lib/kim/Install.py
index 8fbaaffb7f..0c9d717bc3 100644
--- a/lib/kim/Install.py
+++ b/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):
diff --git a/lib/kim/KIM_LAMMPS_PlugIn.h b/lib/kim/KIM_LAMMPS_PlugIn.h
new file mode 100644
index 0000000000..33706e220d
--- /dev/null
+++ b/lib/kim/KIM_LAMMPS_PlugIn.h
@@ -0,0 +1,210 @@
+// 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
diff --git a/lib/kim/Makefile.lammps b/lib/kim/Makefile.lammps
index dc2a6b78d4..39afb1286a 100644
--- a/lib/kim/Makefile.lammps
+++ b/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=\"$(KIM_INSTALL_DIR)\"
+kim_SYSLIB = -ldl
kim_SYSPATH =
diff --git a/lib/kim/README b/lib/kim/README
index bf1148ed10..ce4ea1bdff 100644
--- a/lib/kim/README
+++ b/lib/kim/README
@@ -20,11 +20,11 @@ Instructions:
1. Configure lammps for use with the kim-api library installed in this directory
-$ 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.
diff --git a/lib/kim/pair-kim.release.info b/lib/kim/pair-kim.release.info
deleted file mode 100644
index f6c3c01c4e..0000000000
--- a/lib/kim/pair-kim.release.info
+++ /dev/null
@@ -1,6 +0,0 @@
-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.
diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index b92b07e23f..57bb6cb894 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -27,7 +27,6 @@
// includes from LAMMPS
#include "pair_kim.h"
-#include "pair_kim_version.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
@@ -39,201 +38,13 @@
#include "domain.h"
#include "error.h"
-// includes from KIM
-#include "dlfcn.h"
-
-#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 "KIM_LAMMPS_PlugIn.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-void * PairKIM::kim_api_library = NULL;
-bool PairKIM::kim_api_is_strictly_between_1_5_and_2_0;
-int (*PairKIM::report_error)(int line, const char *, const char *, int) = NULL;
-void (*PairKIM::kim_api_setm_compute_by_index)(void *, int *, ...) = NULL;
-int (*PairKIM::kim_api_model_compute)(void *);
-int (*PairKIM::kim_api_model_init)(void *);
-int (*PairKIM::kim_api_model_reinit)(void *);
-void * (*PairKIM::kim_api_get_sim_buffer)(void *, int *);
-void * (*PairKIM::kim_api_get_data_by_index)(void *, int, int *);
-int (*PairKIM::kim_api_model_destroy)(void *);
-void (*PairKIM::kim_api_free)(void *, int *);
-int (*PairKIM::kim_api_string_init)(void *, const char *, const char *);
-int (*PairKIM::kim_api_is_half_neighbors)(void *, int *);
-int (*PairKIM::kim_api_get_NBC_method)(void *, const char **);
-int (*PairKIM::kim_api_get_index)(void *, const char *, int *);
-int (*PairKIM::kim_api_getm_index)(void *, int *, int, ...);
-int (*PairKIM::kim_api_get_species_code)(void *, const char *, int *);
-void (*PairKIM::kim_api_setm_data_by_index)(void *, int *, int, ...);
-int (*PairKIM::kim_api_set_method_by_index)(void *, int, intptr_t, void (*)());
-void (*PairKIM::kim_api_set_sim_buffer)(void *, void *, int *);
-int (*PairKIM::kim_api_set_data_by_index)(void *, int, intptr_t, void *);
-void (*PairKIM::kim_api_set_compute_by_index)(void *, int, int, int*);
-int (*PairKIM::kim_api_get_num_params)(void *, int *, int *);
-int (*PairKIM::kim_api_get_free_parameter)(void *, const int, const char **);
-void * (*PairKIM::kim_api_get_data)(void *, const char *, int *);
-intptr_t (*PairKIM::kim_api_get_rank)(void *, const char *, int *);
-intptr_t (*PairKIM::kim_api_get_shape)(void *, const char *, int *, int *);
-int (*PairKIM::kim_api_model_info)(void *, const char *);
-
-bool PairKIM::setup_kim_api_library()
-{
- if (kim_api_library == NULL)
- {
-#ifdef KIM_INSTALL_DIR
- kim_api_library = dlopen(KIM_INSTALL_DIR "/lib/libkim-api-v1.so", RTLD_NOW);
-#endif
-
- if (kim_api_library == NULL)
- kim_api_library = dlopen("kim-api-v1.so", RTLD_NOW);
-
- if (kim_api_library == NULL)
- {
- error->all(FLERR,"KIM API library cannot be found");
- return false;
- }
- else
- {
- // check for version and set kim_api_is_strictly_between_1_5_and_2_0
- void * ver = dlsym(kim_api_library, "KIM_API_get_version");
- if (ver == NULL)
- kim_api_is_strictly_between_1_5_and_2_0 = false;
- else
- kim_api_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(kim_api_library, "KIM_API_report_error")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_setm_compute_by_index =
- (void (*)(void *, int *, ...))
- dlsym(kim_api_library, "KIM_API_setm_compute_by_index")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_model_compute = (int (*)(void *))
- dlsym(kim_api_library, "KIM_API_model_compute")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_model_init = (int (*)(void *))
- dlsym(kim_api_library, "KIM_API_model_init")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_model_reinit = (int (*)(void *))
- dlsym(kim_api_library, "KIM_API_model_reinit")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_sim_buffer = (void * (*)(void *, int *))
- dlsym(kim_api_library, "KIM_API_get_sim_buffer")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_data_by_index = (void * (*)(void *, int, int *))
- dlsym(kim_api_library, "KIM_API_get_data_by_index")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_model_destroy = (int (*)(void *))
- dlsym(kim_api_library, "KIM_API_model_destroy")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_free = (void (*)(void *, int *))
- dlsym(kim_api_library, "KIM_API_free")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_string_init =
- (int (*)(void *, const char *, const char *))
- dlsym(kim_api_library, "KIM_API_string_init")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_is_half_neighbors = (int (*)(void *, int *))
- dlsym(kim_api_library, "KIM_API_is_half_neighbors")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_NBC_method = (int (*)(void *, const char **))
- dlsym(kim_api_library, "KIM_API_get_NBC_method")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_index = (int (*)(void *, const char *, int *))
- dlsym(kim_api_library, "KIM_API_get_index")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_getm_index = (int (*)(void *, int *, int, ...))
- dlsym(kim_api_library, "KIM_API_getm_index")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_species_code =
- (int (*)(void *, const char *, int *))
- dlsym(kim_api_library, "KIM_API_get_species_code")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_setm_data_by_index =
- (void (*)(void *, int *, int, ...))
- dlsym(kim_api_library, "KIM_API_setm_data_by_index")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_set_method_by_index =
- (int (*)(void *, int, intptr_t, void (*)()))
- dlsym(kim_api_library, "KIM_API_set_method_by_index")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_set_sim_buffer = (void (*)(void *, void *, int *))
- dlsym(kim_api_library, "KIM_API_set_sim_buffer")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_set_data_by_index =
- (int (*)(void *, int, intptr_t, void *))
- dlsym(kim_api_library, "KIM_API_set_data_by_index")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_set_compute_by_index =
- (void (*)(void *, int, int, int*))
- dlsym(kim_api_library, "KIM_API_set_compute_by_index")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_num_params = (int (*)(void *, int *, int *))
- dlsym(kim_api_library, "KIM_API_get_num_params")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_free_parameter =
- (int (*)(void *, const int, const char **))
- dlsym(kim_api_library, "KIM_API_get_free_parameter")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_data = (void * (*)(void *, const char *, int *))
- dlsym(kim_api_library, "KIM_API_get_data")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_rank =
- (intptr_t (*)(void *, const char *, int *))
- dlsym(kim_api_library, "KIM_API_get_rank")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_get_shape =
- (intptr_t (*)(void *, const char *, int *, int *))
- dlsym(kim_api_library, "KIM_API_get_shape")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- if (NULL == (kim_api_model_info = (int (*)(void *, const char *))
- dlsym(kim_api_library, "KIM_API_model_info")))
- error->all(FLERR,(error_prefix + std::string(dlerror())).c_str());
-
- return true;
- }
- }
- else
- {
- return true;
- }
-}
+void * (*PairKIM::kim_get_sim_buffer)(void *, int *);
PairKIM::PairKIM(LAMMPS *lmp) :
Pair(lmp),
@@ -244,6 +55,7 @@ PairKIM::PairKIM(LAMMPS *lmp) :
lmps_unique_elements(0),
lmps_num_unique_elements(0),
lmps_units(METAL),
+ kim(new KIM_LAMMPS_PlugIn),
pkim(0),
kim_ind_coordinates(-1),
kim_ind_numberOfParticles(-1),
@@ -286,7 +98,7 @@ PairKIM::PairKIM(LAMMPS *lmp) :
PairKIM::~PairKIM()
{
- if (kim_api_library != NULL)
+ if (kim->library != NULL)
{
// clean up kim_modelname
if (kim_modelname != 0) delete [] kim_modelname;
@@ -316,9 +128,11 @@ PairKIM::~PairKIM()
// clean up KIM interface (if necessary)
kim_free();
- dlclose(kim_api_library);
+ dlclose(kim->library);
}
+ delete kim;
+
return;
}
@@ -365,17 +179,17 @@ void PairKIM::compute(int eflag , int vflag)
// pass current atom pointers to KIM
set_volatiles();
- kim_api_setm_compute_by_index(pkim, &kimerror,3*3,
- kim_ind_particleEnergy, eflag_atom,
- (int) kim_model_has_particleEnergy,
- kim_ind_particleVirial, vflag_atom,
- (int) kim_model_has_particleVirial,
- kim_ind_virial, vflag_global!=0,
- no_virial_fdotr_compute);
+ kim->setm_compute_by_index(pkim, &kimerror,3*3,
+ kim_ind_particleEnergy, eflag_atom,
+ (int) kim_model_has_particleEnergy,
+ kim_ind_particleVirial, vflag_atom,
+ (int) kim_model_has_particleVirial,
+ kim_ind_virial, vflag_global!=0,
+ no_virial_fdotr_compute);
kim_error(__LINE__,"setm_compute_by_index",kimerror);
// compute via KIM model
- kimerror = kim_api_model_compute(pkim);
+ kimerror = kim->model_compute(pkim);
kim_error(__LINE__,"PairKIM::pkim->model_compute() error",kimerror);
// assemble force and particleVirial if needed
if (!lmps_using_newton) comm->reverse_comm_pair(this);
@@ -452,7 +266,8 @@ void PairKIM::settings(int narg, char **arg)
// This is called when "pair_style kim ..." is read from input
// may be called multiple times
- setup_kim_api_library(); // exits on failure
+ kim->setup_kim_api_library(error); // exits on failure
+ kim_get_sim_buffer = kim->get_sim_buffer;
++settings_call_count;
init_style_call_count = 0;
@@ -603,7 +418,7 @@ void PairKIM::init_style()
if (!kim_init_ok)
{
kim_init();
- kimerror = kim_api_model_init(pkim);
+ kimerror = kim->model_init(pkim);
if (kimerror != KIM_STATUS_OK)
kim_error(__LINE__, "KIM API:model_init() failed", kimerror);
else
@@ -675,7 +490,7 @@ void PairKIM::reinit()
// Then reinit KIM model
int kimerror;
- kimerror = kim_api_model_reinit(pkim);
+ kimerror = kim->model_reinit(pkim);
kim_error(__LINE__,"model_reinit unsuccessful", kimerror);
}
@@ -817,7 +632,7 @@ double PairKIM::memory_usage()
void PairKIM::kim_error(int ln, const char* msg, int errcode)
{
if (errcode == KIM_STATUS_OK) return;
- report_error(ln,(char *) __FILE__, (char *) msg,errcode);
+ kim->report_error(ln,(char *) __FILE__, (char *) msg,errcode);
error->all(__FILE__,ln,"Internal KIM error");
return;
@@ -831,7 +646,7 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
void * pkim = *kimmdl;
int kimerror;
- PairKIM *self = (PairKIM *) kim_api_get_sim_buffer(pkim, &kimerror);
+ PairKIM *self = (PairKIM *) kim_get_sim_buffer(pkim, &kimerror);
if (self->kim_model_using_Rij) {
*pRij = &(self->Rij[0]);
@@ -882,8 +697,8 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
// set Rij if needed
if (self->kim_model_using_Rij) {
double* x = (double *)
- kim_api_get_data_by_index(pkim, self->kim_ind_coordinates,
- &kimerror);
+ self->kim->get_data_by_index(pkim, self->kim_ind_coordinates,
+ &kimerror);
for (jj=0; jj < *numnei; jj++) {
int i = *atom;
j = (*nei1atom)[jj];
@@ -930,8 +745,8 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request,
// set Rij if needed
if (self->kim_model_using_Rij){
double* x = (double *)
- kim_api_get_data_by_index(pkim, self->kim_ind_coordinates,
- &kimerror);
+ self->kim->get_data_by_index(pkim, self->kim_ind_coordinates,
+ &kimerror);
for(int jj=0; jj < *numnei; jj++){
int i = *atom;
int j = (*nei1atom)[jj];
@@ -962,12 +777,12 @@ void PairKIM::kim_free()
if (kim_model_init_ok)
{
- kimerror = kim_api_model_destroy(pkim);
+ kimerror = kim->model_destroy(pkim);
kim_model_init_ok = false;
}
if (kim_init_ok)
{
- kim_api_free(&pkim, &kimerror);
+ kim->free(&pkim, &kimerror);
kim_init_ok = false;
}
if (pkim != 0)
@@ -1006,7 +821,7 @@ void PairKIM::kim_init()
}
// initialize KIM model
- kimerror = kim_api_string_init(&pkim, test_descriptor_string, kim_modelname);
+ kimerror = kim->string_init(&pkim, test_descriptor_string, kim_modelname);
if (kimerror != KIM_STATUS_OK)
kim_error(__LINE__,"KIM initialization failed", kimerror);
else
@@ -1019,10 +834,10 @@ void PairKIM::kim_init()
// determine kim_model_using_* true/false values
//
// check for half or full list
- kim_model_using_half = kim_api_is_half_neighbors(pkim, &kimerror);
+ kim_model_using_half = kim->is_half_neighbors(pkim, &kimerror);
//
const char* NBC_method;
- kimerror = kim_api_get_NBC_method(pkim, &NBC_method);
+ kimerror = kim->get_NBC_method(pkim, &NBC_method);
kim_error(__LINE__,"NBC method not set",kimerror);
// check for CLUSTER mode
kim_model_using_cluster = (strcmp(NBC_method,"CLUSTER")==0);
@@ -1031,18 +846,18 @@ void PairKIM::kim_init()
(strcmp(NBC_method,"NEIGH_RVEC_F")==0));
// get correct index of each variable in kim_api object
- kim_api_getm_index(pkim, &kimerror, 3*15,
+ kim->getm_index(pkim, &kimerror, 3*15,
"coordinates", &kim_ind_coordinates, 1,
"cutoff", &kim_ind_cutoff, 1,
"numberOfParticles", &kim_ind_numberOfParticles, 1,
"numberParticleTypes", &kim_ind_numberOfSpecies,
- ! kim_api_is_strictly_between_1_5_and_2_0,
+ ! kim->is_strictly_between_1_5_and_2_0,
"particleTypes", &kim_ind_particleSpecies,
- ! kim_api_is_strictly_between_1_5_and_2_0,
+ ! kim->is_strictly_between_1_5_and_2_0,
"numberOfSpecies", &kim_ind_numberOfSpecies,
- kim_api_is_strictly_between_1_5_and_2_0,
+ kim->is_strictly_between_1_5_and_2_0,
"particleSpecies", &kim_ind_particleSpecies,
- kim_api_is_strictly_between_1_5_and_2_0,
+ kim->is_strictly_between_1_5_and_2_0,
"numberContributingParticles", &kim_ind_numberContributingParticles,
kim_model_using_half,
"particleEnergy", &kim_ind_particleEnergy,
@@ -1062,7 +877,7 @@ void PairKIM::kim_init()
for(int i = 0; i < lmps_num_unique_elements; i++){
int kimerror;
kim_particle_codes[i]
- = kim_api_get_species_code(pkim, lmps_unique_elements[i], &kimerror);
+ = kim->get_species_code(pkim, lmps_unique_elements[i], &kimerror);
kim_error(__LINE__, "create_kim_particle_codes: symbol not found ",
kimerror);
}
@@ -1081,7 +896,7 @@ void PairKIM::set_statics()
lmps_local_tot_num_atoms = (int) (atom->nghost + atom->nlocal);
int kimerror;
- kim_api_setm_data_by_index(pkim, &kimerror, 4*6,
+ kim->setm_data_by_index(pkim, &kimerror, 4*6,
kim_ind_numberOfSpecies, 1, (void *) &(atom->ntypes), 1,
kim_ind_cutoff, 1, (void *) &(kim_global_cutoff), 1,
kim_ind_numberOfParticles, 1, (void *) &lmps_local_tot_num_atoms, 1,
@@ -1092,13 +907,12 @@ void PairKIM::set_statics()
kim_error(__LINE__, "setm_data_by_index", kimerror);
if (!kim_model_using_cluster)
{
- kimerror = kim_api_set_method_by_index(pkim, kim_ind_get_neigh, 1,
- (void (*)()) &get_neigh);
+ kimerror = kim->set_method_by_index(pkim, kim_ind_get_neigh, 1,
+ (void (*)()) &get_neigh);
kim_error(__LINE__, "set_method_by_index", kimerror);
}
-
- kim_api_set_sim_buffer(pkim, (void *)this, &kimerror);
+ kim->set_sim_buffer(pkim, (void *)this, &kimerror);
kim_error(__LINE__, "set_sim_buffer", kimerror);
return;
@@ -1112,33 +926,33 @@ void PairKIM::set_volatiles()
lmps_local_tot_num_atoms = (int) (atom->nghost + atom->nlocal);
intptr_t nall = (intptr_t) lmps_local_tot_num_atoms;
- kim_api_setm_data_by_index(pkim, &kimerror, 4*2,
+ kim->setm_data_by_index(pkim, &kimerror, 4*2,
kim_ind_coordinates, 3*nall, (void*) &(atom->x[0][0]), 1,
kim_ind_particleSpecies, nall, (void*) kim_particleSpecies, 1);
kim_error(__LINE__, "setm_data_by_index", kimerror);
if (kim_model_has_particleEnergy && (eflag_atom == 1))
{
- kimerror = kim_api_set_data_by_index(pkim, kim_ind_particleEnergy, nall,
- (void*) eatom);
+ kimerror = kim->set_data_by_index(pkim, kim_ind_particleEnergy, nall,
+ (void*) eatom);
kim_error(__LINE__, "set_data_by_index", kimerror);
}
if (kim_model_has_particleVirial && (vflag_atom == 1))
{
- kimerror = kim_api_set_data_by_index(pkim, kim_ind_particleVirial, 6*nall,
- (void*) &(vatom[0][0]));
+ kimerror = kim->set_data_by_index(pkim, kim_ind_particleVirial, 6*nall,
+ (void*) &(vatom[0][0]));
kim_error(__LINE__, "set_data_by_index", kimerror);
}
if (kim_model_has_forces)
{
if (lmps_hybrid)
- kimerror = kim_api_set_data_by_index(pkim, kim_ind_forces, nall*3,
- (void*) &(lmps_force_tmp[0][0]));
+ kimerror = kim->set_data_by_index(pkim, kim_ind_forces, nall*3,
+ (void*) &(lmps_force_tmp[0][0]));
else
- kimerror = kim_api_set_data_by_index(pkim, kim_ind_forces, nall*3,
- (void*) &(atom->f[0][0]));
+ kimerror = kim->set_data_by_index(pkim, kim_ind_forces, nall*3,
+ (void*) &(atom->f[0][0]));
kim_error(__LINE__, "setm_data_by_index", kimerror);
}
@@ -1151,17 +965,17 @@ void PairKIM::set_volatiles()
if (kim_model_has_particleVirial)
{
if(vflag_atom != 1) {
- kim_api_set_compute_by_index(pkim, kim_ind_particleVirial,
- KIM_COMPUTE_FALSE, &kimerror);
+ kim->set_compute_by_index(pkim, kim_ind_particleVirial,
+ KIM_COMPUTE_FALSE, &kimerror);
} else {
- kim_api_set_compute_by_index(pkim, kim_ind_particleVirial,
- KIM_COMPUTE_TRUE, &kimerror);
+ kim->set_compute_by_index(pkim, kim_ind_particleVirial,
+ KIM_COMPUTE_TRUE, &kimerror);
}
}
if (no_virial_fdotr_compute == 1)
{
- kim_api_set_compute_by_index(pkim, kim_ind_virial,
+ kim->set_compute_by_index(pkim, kim_ind_virial,
((vflag_global != 1) ? KIM_COMPUTE_FALSE : KIM_COMPUTE_TRUE),
&kimerror);
}
@@ -1222,34 +1036,34 @@ void PairKIM::set_kim_model_has_flags()
int kimerror;
// get KIM API object representing the KIM Model only
- kimerror = kim_api_model_info(&pkim, kim_modelname);
+ kimerror = kim->model_info(&pkim, kim_modelname);
kim_error(__LINE__,"KIM initialization failed", kimerror);
// determine if the KIM Model can compute the total energy
- kim_api_get_index(pkim, (char*) "energy", &kimerror);
+ kim->get_index(pkim, (char*) "energy", &kimerror);
kim_model_has_energy = (kimerror == KIM_STATUS_OK);
if (!kim_model_has_energy)
error->warning(FLERR,"KIM Model does not provide `energy'; "
"Potential energy will be zero");
// determine if the KIM Model can compute the forces
- kim_api_get_index(pkim, (char*) "forces", &kimerror);
+ kim->get_index(pkim, (char*) "forces", &kimerror);
kim_model_has_forces = (kimerror == KIM_STATUS_OK);
if (!kim_model_has_forces)
error->warning(FLERR,"KIM Model does not provide `forces'; "
"Forces will be zero");
// determine if the KIM Model can compute the particleEnergy
- kim_api_get_index(pkim, (char*) "particleEnergy", &kimerror);
+ kim->get_index(pkim, (char*) "particleEnergy", &kimerror);
kim_model_has_particleEnergy = (kimerror == KIM_STATUS_OK);
if (!kim_model_has_particleEnergy)
error->warning(FLERR,"KIM Model does not provide `particleEnergy'; "
"energy per atom will be zero");
// determine if the KIM Model can compute the particleVerial
- kim_api_get_index(pkim, (char*) "particleVirial", &kimerror);
+ kim->get_index(pkim, (char*) "particleVirial", &kimerror);
kim_model_has_particleVirial = (kimerror == KIM_STATUS_OK);
- kim_api_get_index(pkim, (char*) "process_dEdr", &kimerror);
+ kim->get_index(pkim, (char*) "process_dEdr", &kimerror);
kim_model_has_particleVirial = kim_model_has_particleVirial ||
(kimerror == KIM_STATUS_OK);
if (!kim_model_has_particleVirial)
@@ -1257,7 +1071,7 @@ void PairKIM::set_kim_model_has_flags()
"virial per atom will be zero");
// tear down KIM API object
- kim_api_free(&pkim, &kimerror);
+ kim->free(&pkim, &kimerror);
// now destructor will do the remaining tear down for mdl
return;
@@ -1293,7 +1107,7 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
"#\n"
"\n");
- if (kim_api_is_strictly_between_1_5_and_2_0)
+ if (kim->is_strictly_between_1_5_and_2_0)
strcat(*test_descriptor_string,
"KIM_API_Version := 1.6.0\n\n");
@@ -1344,7 +1158,7 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
}
// Write Supported species section
- if (kim_api_is_strictly_between_1_5_and_2_0)
+ if (kim->is_strictly_between_1_5_and_2_0)
strcat(*test_descriptor_string,
"\n"
"PARTICLE_SPECIES:\n");
@@ -1403,7 +1217,7 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
"# Name Type Unit Shape\n"
"numberOfParticles integer none []\n"
"numberContributingParticles integer none []\n");
- if (kim_api_is_strictly_between_1_5_and_2_0)
+ if (kim->is_strictly_between_1_5_and_2_0)
strcat(*test_descriptor_string,
"numberOfSpecies integer none []\n"
"particleSpecies integer none ");
@@ -1510,13 +1324,13 @@ void *PairKIM::extract(const char *str, int &dim)
// check to make sure that the requested parameter is a valid free parameter
- kimerror = kim_api_get_num_params(pkim, &numParams, &dummyint);
+ kimerror = kim->get_num_params(pkim, &numParams, &dummyint);
kim_error(__LINE__, "get_num_free_params", kimerror);
char **freeParamNames = new char*[numParams];
for (int k = 0; k < numParams; k++)
{
- kimerror = kim_api_get_free_parameter(pkim, k,
- (const char**) &freeParamNames[k]);
+ kimerror = kim->get_free_parameter(pkim, k,
+ (const char**) &freeParamNames[k]);
kim_error(__LINE__, "get_free_parameter", kimerror);
if (0 == strcmp(paramName, freeParamNames[k]))
{
@@ -1534,7 +1348,7 @@ void *PairKIM::extract(const char *str, int &dim)
}
// get the parameter arry from pkim object
- paramData = kim_api_get_data(pkim, paramName, &kimerror);
+ paramData = kim->get_data(pkim, paramName, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
delete [] speciesIndex, speciesIndex = 0;
@@ -1543,7 +1357,7 @@ void *PairKIM::extract(const char *str, int &dim)
kim_error(__LINE__,"get_data",kimerror);
// get rank and shape of parameter
- rank = kim_api_get_rank(pkim, paramName, &kimerror);
+ rank = kim->get_rank(pkim, paramName, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
delete [] speciesIndex, speciesIndex = 0;
@@ -1552,7 +1366,7 @@ void *PairKIM::extract(const char *str, int &dim)
kim_error(__LINE__,"get_rank",kimerror);
int *shape = new int[maxLine];
- dummyint = kim_api_get_shape(pkim, paramName, shape, &kimerror);
+ dummyint = kim->get_shape(pkim, paramName, shape, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
delete [] speciesIndex, speciesIndex = 0;
diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h
index 027d37e7fc..3b12cbe8b0 100644
--- a/src/KIM/pair_kim.h
+++ b/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 *);
};
}
--
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