First working version of pair_kim with kim-api-v2 (8bbba228) · Commits · 郑智淋 / lammps

lib/kim/Install.py

+4 −4

Original line number	Diff line number	Diff line
		@@ -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-v1.9.5 (current as of May 2018)
		default = kim-api-v2.0.0-beta.0 (current as of June 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.
		@@ -109,7 +109,7 @@ nargs = len(args)
		if nargs == 0: error()

		thisdir = os.environ['PWD']
		version = "kim-api-v1.9.5"
		version = "kim-api-v2.0.0-beta.0"

		buildflag = False
		everythingflag = False
		@@ -234,7 +234,7 @@ if buildflag:
		# add all OpenKIM models, if desired
		if everythingflag:
		print("Adding all OpenKIM models, this will take a while ...")
		cmd = '%s/bin/kim-api-v1-collections-management install system OpenKIM' % (kimdir)
		cmd = '%s/bin/kim-api-v2-collections-management install system OpenKIM' % (kimdir)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if verboseflag: print(txt.decode("UTF-8"))

		@@ -251,6 +251,6 @@ if addflag:
		error()

		# download single model
		cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
		cmd = '%s/bin/kim-api-v2-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if verboseflag: print (txt.decode("UTF-8"))

lib/kim/Makefile.lammps

+3 −3

Original line number	Diff line number	Diff line
		@@ -18,10 +18,10 @@

		include ../../lib/kim/Makefile.KIM_DIR

		ifeq ($(wildcard $(KIM_INSTALL_DIR)/bin/kim-api-v1-build-config),)
		KIM_CONFIG_HELPER = kim-api-v1-build-config
		ifeq ($(wildcard $(KIM_INSTALL_DIR)/bin/kim-api-v2-build-config),)
		KIM_CONFIG_HELPER = kim-api-v2-build-config
		else
		KIM_CONFIG_HELPER = $(KIM_INSTALL_DIR)/bin/kim-api-v1-build-config
		KIM_CONFIG_HELPER = $(KIM_INSTALL_DIR)/bin/kim-api-v2-build-config
		endif
		ifeq ($(shell $(KIM_CONFIG_HELPER) --version 2> /dev/null),)
		$(error $(KIM_CONFIG_HELPER) utility is not available. Something is wrong with your KIM API package setup)

src/KIM/pair_kim.cpp

+267 −418

File changed.

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src/KIM/pair_kim.h

+19 −21

Original line number	Diff line number	Diff line
		@@ -33,6 +33,7 @@ PairStyle(kim,PairKIM)
		// includes from KIM & LAMMPS
		class KIM_API_model;
		#include "pair.h"
		#include "KIM_SimulatorHeaders.hpp"


		namespace LAMMPS_NS {
		@@ -61,7 +62,6 @@ namespace LAMMPS_NS {

		// values set in settings()
		char* kim_modelname;
		bool print_kim_file;

		// values set in coeff()

		@@ -79,29 +79,23 @@ namespace LAMMPS_NS {
		bool lmps_using_molecular;
		enum unit_sys {REAL, METAL, SI, CGS, ELECTRON};
		unit_sys lmps_units;
		KIM::LengthUnit lengthUnit;
		KIM::EnergyUnit energyUnit;
		KIM::ChargeUnit chargeUnit;
		KIM::TemperatureUnit temperatureUnit;
		KIM::TimeUnit timeUnit;

		// values set in set_kim_model_has_flags(), called by kim_init()
		KIM_API_model* pkim;
		KIM::Model * pkim;
		KIM::ComputeArguments * pargs;
		bool kim_model_has_energy;
		bool kim_model_has_forces;
		bool kim_model_has_virial;
		bool kim_model_has_particleEnergy;
		bool kim_model_has_particleVirial;

		// values set in kim_init(), after call to string_init(_)
		bool kim_init_ok;
		int kim_ind_coordinates;
		int kim_ind_numberOfParticles;
		int kim_ind_numberContributingParticles;
		int kim_ind_numberOfSpecies;
		int kim_ind_particleSpecies;
		int kim_ind_get_neigh;
		int kim_ind_neighObject;
		int kim_ind_cutoff;
		int kim_ind_energy;
		int kim_ind_particleEnergy;
		int kim_ind_forces;
		int kim_ind_virial;
		int kim_ind_particleVirial;

		// values set in init_style(), after calling pkim->model_init()
		bool kim_model_init_ok;
		@@ -111,27 +105,31 @@ namespace LAMMPS_NS {
		// values set in set_statics(), called at end of kim_init(),
		// then again in set_volatiles(), called in compute()
		int lmps_local_tot_num_atoms;
		double kim_global_cutoff; // KIM Model cutoff value
		double kim_global_influence_distance; // KIM Model cutoff value
		int kim_number_of_cutoffs;
		double const * kim_cutoff_values;

		// values set in compute()
		int lmps_maxalloc; // max allocated memory value
		int* kim_particleSpecies; // array of KIM particle species
		int* kim_particleContributing; // array of KIM particle contributing
		int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS
		// is in molecular mode

		// KIM specific helper functions
		void kim_error(int, const char *, int);
		void kim_init();
		void kim_free();
		void set_statics();
		void set_volatiles();
		void set_lmps_flags();
		void set_kim_model_has_flags();
		void write_descriptor(char** test_descriptor_string);
		// static methods used as callbacks from KIM
		static int get_neigh(void** kimmdl, int* mode, int* request,
		int* atom, int* numnei, int** nei1atom,
		double** pRij);
		static int get_neigh(
		void const * const dataObject,
		int const numberOfCutoffs, double const * const cutoffs,
		int const neighborListIndex, int const particleNumber,
		int * const numberOfNeighbors,
		int const ** const neighborsOfParticle);
		};
		}

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