add unit conversion to table pair style (2acf71c3) · Commits · 郑智淋 / lammps

src/pair_table.cpp

+25 −21

Original line number	Diff line number	Diff line
		@@ -44,6 +44,7 @@ PairTable::PairTable(LAMMPS *lmp) : Pair(lmp)
		{
		ntables = 0;
		tables = NULL;
		unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
		}

		/* ---------------------------------------------------------------------- */
		@@ -360,6 +361,12 @@ void PairTable::read_table(Table tb, char file, char *keyword)
		{
		TableFileReader reader(lmp, file, "pair");

		// transparently convert units for supported conversions

		int unit_convert = reader.get_unit_convert();
		double conversion_factor = utils::get_conversion_factor(utils::ENERGY,
		unit_convert);

		char *line = reader.find_section_start(keyword);

		if (!line) {
		@@ -404,8 +411,8 @@ void PairTable::read_table(Table tb, char file, char *keyword)
		ValueTokenizer values(line);
		values.next_int();
		rfile = values.next_double();
		tb->efile[i] = values.next_double();
		tb->ffile[i] = values.next_double();
		tb->efile[i] = conversion_factor * values.next_double();
		tb->ffile[i] = conversion_factor * values.next_double();
		} catch (TokenizerException & e) {
		++cerror;
		}
		@@ -461,29 +468,26 @@ void PairTable::read_table(Table tb, char file, char *keyword)
		}
		}

		if (ferror) {
		std::string str = fmt::format("{} of {} force values in table are inconsistent with -dE/dr.\n"
		" Should only be flagged at inflection points",ferror,tb->ninput);
		error->warning(FLERR,str.c_str());
		}
		if (ferror)
		error->warning(FLERR,fmt::format("{} of {} force values in table are "
		"inconsistent with -dE/dr.\n Should "
		"only be flagged at inflection points",
		ferror,tb->ninput));

		// warn if re-computed distance values differ from file values

		if (rerror) {
		char str[128];
		sprintf(str,"%d of %d distance values in table with relative error\n"
		" over %g to re-computed values",rerror,tb->ninput,EPSILONR);
		error->warning(FLERR,str);
		}
		if (rerror)
		error->warning(FLERR,fmt::format("{} of {} distance values in table with "
		"relative error\n over {} to "
		"re-computed values",
		rerror,tb->ninput,EPSILONR));

		// warn if data was read incompletely, e.g. columns were missing

		if (cerror) {
		char str[128];
		sprintf(str,"%d of %d lines in table were incomplete\n"
		" or could not be parsed completely",cerror,tb->ninput);
		error->warning(FLERR,str);
		}
		if (cerror)
		error->warning(FLERR,fmt::format("{} of {} lines in table were "
		"incomplete\n or could not be parsed "
		"completely",cerror,tb->ninput));
		}

		/* ----------------------------------------------------------------------

src/table_file_reader.cpp

+6 −5

Original line number	Diff line number	Diff line
		@@ -28,8 +28,9 @@ using namespace LAMMPS_NS;

		TableFileReader::TableFileReader(LAMMPS *lmp,
		const std::string &filename,
		const std::string &type) :
		PotentialFileReader(lmp, filename, type + " table")
		const std::string &type,
		const int auto_convert) :
		PotentialFileReader(lmp, filename, type + " table", auto_convert)
		{
		}

src/table_file_reader.h

+3 −2

Original line number	Diff line number	Diff line
		@@ -24,7 +24,8 @@ namespace LAMMPS_NS
		{
		class TableFileReader : public PotentialFileReader {
		public:
		TableFileReader(class LAMMPS *lmp, const std::string &filename, const std::string & type);
		TableFileReader(class LAMMPS *lmp, const std::string &filename,
		const std::string &type, const int auto_convert = 0);
		virtual ~TableFileReader();

		char *find_section_start(const std::string &keyword);

src/utils.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -687,7 +687,7 @@ double utils::get_conversion_factor(const int property, const int conversion)
		} else if (conversion == METAL2REAL) {
		return 23.060549;
		} else if (conversion == REAL2METAL) {
		return 0.04336410204284381954;
		return 1.0/23.060549;
		}
		}
		return 0.0;

unittest/formats/test_pair_unit_convert.cpp

+105 −0

Original line number	Diff line number	Diff line
		@@ -140,6 +140,10 @@ TEST_F(PairUnitConvertTest, lj_cut)
		lmp->input->one("read_data test_pair_unit_convert.data");
		lmp->input->one("pair_style lj/cut 6.0");
		lmp->input->one("pair_coeff * * 0.01014286346782117 2.0");
		remove("test.table.metal");
		lmp->input->one("pair_write 1 1 1000 r 0.1 6.0 test.table.metal lj_1_1");
		lmp->input->one("pair_write 1 2 1000 r 0.1 6.0 test.table.metal lj_1_2");
		lmp->input->one("pair_write 2 2 1000 r 0.1 6.0 test.table.metal lj_2_2");
		lmp->input->one("run 0 post no");
		if (!verbose) ::testing::internal::GetCapturedStdout();

		@@ -158,6 +162,10 @@ TEST_F(PairUnitConvertTest, lj_cut)
		lmp->input->one("read_data test_pair_unit_convert.data");
		lmp->input->one("pair_style lj/cut 6.0");
		lmp->input->one("pair_coeff * * 0.2339 2.0");
		remove("test.table.real");
		lmp->input->one("pair_write 1 1 1000 r 0.1 6.0 test.table.real lj_1_1");
		lmp->input->one("pair_write 1 2 1000 r 0.1 6.0 test.table.real lj_1_2");
		lmp->input->one("pair_write 2 2 1000 r 0.1 6.0 test.table.real lj_2_2");
		lmp->input->one("run 0 post no");
		if (!verbose) ::testing::internal::GetCapturedStdout();

		@@ -216,6 +224,101 @@ TEST_F(PairUnitConvertTest, sw)
		EXPECT_NEAR(ev_convert * fold[i][j], f[i][j], fabs(f[i][j] * rel_error));
		}

		TEST_F(PairUnitConvertTest, table_metal2real)
		{
		// check if the prerequisite pair style is available
		if (!info->has_style("pair", "table")) GTEST_SKIP();

		if (!verbose) ::testing::internal::CaptureStdout();
		lmp->input->one("units metal");
		lmp->input->one("read_data test_pair_unit_convert.data");
		lmp->input->one("pair_style table linear 1000");
		lmp->input->one("pair_coeff 1 1 test.table.metal lj_1_1");
		lmp->input->one("pair_coeff 1 2 test.table.metal lj_1_2");
		lmp->input->one("pair_coeff 2 2 test.table.metal lj_2_2");
		lmp->input->one("run 0 post no");
		if (!verbose) ::testing::internal::GetCapturedStdout();

		// copy pressure, energy, and force from first step
		double pold;
		lmp->output->thermo->evaluate_keyword("press", &pold);
		double eold = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
		double **f = lmp->atom->f;
		for (int i = 0; i < 4; ++i)
		for (int j = 0; j < 3; ++j)
		fold[i][j] = f[i][j];

		if (!verbose) ::testing::internal::CaptureStdout();
		lmp->input->one("clear");
		lmp->input->one("units real");
		lmp->input->one("read_data test_pair_unit_convert.data");
		lmp->input->one("pair_style table linear 1000");
		lmp->input->one("pair_coeff 1 1 test.table.metal lj_1_1");
		lmp->input->one("pair_coeff 1 2 test.table.metal lj_1_2");
		lmp->input->one("pair_coeff 2 2 test.table.metal lj_2_2");
		lmp->input->one("run 0 post no");
		if (!verbose) ::testing::internal::GetCapturedStdout();

		double pnew;
		lmp->output->thermo->evaluate_keyword("press", &pnew);
		EXPECT_NEAR(pold, p_convert * pnew, fabs(pnew * rel_error));
		double enew = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
		EXPECT_NEAR(ev_convert * eold, enew, fabs(enew * rel_error));

		f = lmp->atom->f;
		for (int i = 0; i < 4; ++i)
		for (int j = 0; j < 3; ++j)
		EXPECT_NEAR(ev_convert * fold[i][j], f[i][j], fabs(f[i][j] * rel_error));
		}

		TEST_F(PairUnitConvertTest, table_real2metal)
		{
		// check if the prerequisite pair style is available
		if (!info->has_style("pair", "table")) GTEST_SKIP();

		if (!verbose) ::testing::internal::CaptureStdout();
		lmp->input->one("units real");
		lmp->input->one("read_data test_pair_unit_convert.data");
		lmp->input->one("pair_style table linear 1000");
		lmp->input->one("pair_coeff 1 1 test.table.real lj_1_1");
		lmp->input->one("pair_coeff 1 2 test.table.real lj_1_2");
		lmp->input->one("pair_coeff 2 2 test.table.real lj_2_2");
		lmp->input->one("run 0 post no");
		if (!verbose) ::testing::internal::GetCapturedStdout();

		// copy pressure, energy, and force from first step
		double pold;
		lmp->output->thermo->evaluate_keyword("press", &pold);
		double eold = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
		double **f = lmp->atom->f;
		for (int i = 0; i < 4; ++i)
		for (int j = 0; j < 3; ++j)
		fold[i][j] = f[i][j];

		if (!verbose) ::testing::internal::CaptureStdout();
		lmp->input->one("clear");
		lmp->input->one("units metal");
		lmp->input->one("read_data test_pair_unit_convert.data");
		lmp->input->one("pair_style table linear 1000");
		lmp->input->one("pair_coeff 1 1 test.table.real lj_1_1");
		lmp->input->one("pair_coeff 1 2 test.table.real lj_1_2");
		lmp->input->one("pair_coeff 2 2 test.table.real lj_2_2");
		lmp->input->one("run 0 post no");
		if (!verbose) ::testing::internal::GetCapturedStdout();

		double pnew;
		lmp->output->thermo->evaluate_keyword("press", &pnew);
		EXPECT_NEAR(pold, 1.0/p_convert * pnew, fabs(pnew * rel_error));
		double enew = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
		EXPECT_NEAR(1.0/ev_convert * eold, enew, fabs(enew * rel_error));

		f = lmp->atom->f;
		for (int i = 0; i < 4; ++i)
		for (int j = 0; j < 3; ++j)
		EXPECT_NEAR(1.0/ev_convert * fold[i][j], f[i][j],
		fabs(f[i][j] * rel_error));
		}

		TEST_F(PairUnitConvertTest, tersoff)
		{
		// check if the prerequisite pair style is available
		@@ -539,5 +642,7 @@ int main(int argc, char **argv)

		int rv = RUN_ALL_TESTS();
		MPI_Finalize();
		remove("test.table.metal");
		remove("test.table.real");
		return rv;
		}

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