add unit conversion to pair styles eim, gw, gw/zbl, and nb3b/harmonic (435ac907) · Commits · 郑智淋 / lammps

doc/src/pair_eim.rst

+2 −2

Original line number	Diff line number	Diff line
		@@ -48,7 +48,7 @@ and :math:`sigma_i` are calculated as
		\sigma_i = & \sum_{j=i_1}^{i_N} q_j \cdot \psi_{ij} \left(r_{ij}\right) \\
		E_i\left(q_i,\sigma_i\right) = & \frac{1}{2} \cdot q_i \cdot \sigma_i

		where :math:`\eta_{ji} is a pairwise function describing electron flow from atom
		where :math:`\eta_{ji}` is a pairwise function describing electron flow from atom
		I to atom J, and :math:`\psi_{ij}` is another pairwise function. The multi-body
		nature of the EIM potential is a result of the embedding energy term.
		A complete list of all the pair functions used in EIM is summarized
		@@ -63,7 +63,7 @@ below
		\right.\\
		\eta_{ji} = & A_{\eta,ij}\left(\chi_j-\chi_i\right)f_c\left(r,r_{s,\eta,ij},r_{c,\eta,ij}\right) \\
		\psi_{ij}\left(r\right) = & A_{\psi,ij}\exp\left(-\zeta_{ij}r\right)f_c\left(r,r_{s,\psi,ij},r_{c,\psi,ij}\right) \\
		f_{c}\left(r,r_p,r_c\right) = & 0.510204 \mathrm{erfc}\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204
		f_{c}\left(r,r_p,r_c\right) = & 0.510204 \cdot \mathrm{erfc}\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204

		Here :math:`E_b, r_e, r_(c,\phi), \alpha, \beta, A_(\psi), \zeta, r_(s,\psi),
		r_(c,\psi), A_(\eta), r_(s,\eta), r_(c,\eta), \chi,` and pair function type

potentials/MOH.nb3b.harmonic

+1 −1

Original line number	Diff line number	Diff line
		# DATE: 2016-07-29 UNITS: metal CONTRIBUTOR: Todd Zeitler, tzeitle@sandia.gov CITATION: none
		# DATE: 2016-07-29 UNITS: real CONTRIBUTOR: Todd Zeitler, tzeitle@sandia.gov CITATION: none
		# nb3b/harmonic (nonbonded 3-body harmonic) parameters for various elements
		#
		# multiple entries can be added to this file, LAMMPS reads the ones it needs

src/MANYBODY/pair_eim.cpp

+23 −20

Original line number	Diff line number	Diff line
		@@ -41,6 +41,7 @@ PairEIM::PairEIM(LAMMPS *lmp) : Pair(lmp)
		restartinfo = 0;
		one_coeff = 1;
		manybody_flag = 1;
		unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);

		setfl = NULL;
		nmax = 0;
		@@ -477,7 +478,7 @@ void PairEIM::read_file(char *filename)

		// read potential file
		if( comm->me == 0) {
		EIMPotentialFileReader reader(lmp, filename);
		EIMPotentialFileReader reader(lmp, filename, unit_convert_flag);

		reader.get_global(setfl);

		@@ -1050,14 +1051,18 @@ double PairEIM::memory_usage()
		return bytes;
		}

		EIMPotentialFileReader::EIMPotentialFileReader(LAMMPS * lmp, const std::string & filename) :
		EIMPotentialFileReader::EIMPotentialFileReader(LAMMPS *lmp,
		const std::string &filename,
		const int auto_convert) :
		Pointers(lmp), filename(filename)
		{
		if (comm->me != 0) {
		error->one(FLERR, "EIMPotentialFileReader should only be called by proc 0!");
		}

		FILE * fp = force->open_potential(filename.c_str());
		int unit_convert = auto_convert;
		FILE *fp = force->open_potential(filename.c_str(), &unit_convert);
		conversion_factor = utils::get_conversion_factor(utils::ENERGY,unit_convert);

		if (fp == NULL) {
		error->one(FLERR, fmt::format("cannot open EIM potential file {}", filename));
		@@ -1186,7 +1191,7 @@ void EIMPotentialFileReader::parse(FILE * fp)
		PairData data;
		data.rcutphiA = values.next_double();
		data.rcutphiR = values.next_double();
		data.Eb = values.next_double();
		data.Eb = values.next_double() * conversion_factor;
		data.r0 = values.next_double();
		data.alpha = values.next_double();
		data.beta = values.next_double();
		@@ -1194,7 +1199,7 @@ void EIMPotentialFileReader::parse(FILE * fp)
		data.Asigma = values.next_double();
		data.rq = values.next_double();
		data.rcutsigma = values.next_double();
		data.Ac = values.next_double();
		data.Ac = values.next_double() * conversion_factor;
		data.zeta = values.next_double();
		data.rs = values.next_double();

		@@ -1223,12 +1228,10 @@ void EIMPotentialFileReader::get_global(PairEIM::Setfl * setfl) {
		setfl->rsmall = rsmall;
		}

		void EIMPotentialFileReader::get_element(PairEIM::Setfl * setfl, int i, const std::string & name) {
		if (elements.find(name) == elements.end()) {
		char str[128];
		snprintf(str, 128, "Element %s not defined in EIM potential file", name.c_str());
		error->one(FLERR, str);
		}
		void EIMPotentialFileReader::get_element(PairEIM::Setfl *setfl, int i,
		const std::string &name) {
		if (elements.find(name) == elements.end())
		error->one(FLERR,"Element " + name + " not defined in EIM potential file");

		ElementData &data = elements[name];
		setfl->ielement[i] = data.ielement;
		@@ -1240,14 +1243,14 @@ void EIMPotentialFileReader::get_element(PairEIM::Setfl * setfl, int i, const st
		setfl->q0[i] = data.q0;
		}

		void EIMPotentialFileReader::get_pair(PairEIM::Setfl * setfl, int ij, const std::string & elemA, const std::string & elemB) {
		void EIMPotentialFileReader::get_pair(PairEIM::Setfl *setfl, int ij,
		const std::string &elemA,
		const std::string &elemB) {
		auto p = get_pair(elemA, elemB);

		if (pairs.find(p) == pairs.end()) {
		char str[128];
		snprintf(str, 128, "Pair (%s, %s) not defined in EIM potential file", elemA.c_str(), elemB.c_str());
		error->one(FLERR, str);
		}
		if (pairs.find(p) == pairs.end())
		error->one(FLERR,"Element pair (" + elemA + ", " + elemB
		+ ") is not defined in EIM potential file");

		PairData &data = pairs[p];
		setfl->rcutphiA[ij] = data.rcutphiA;

src/MANYBODY/pair_eim.h

+11 −7

Original line number	Diff line number	Diff line
		@@ -98,17 +98,21 @@ class EIMPotentialFileReader : protected Pointers {
		std::string filename;
		static const int MAXLINE = 1024;
		char line[MAXLINE];
		double conversion_factor;

		void parse(FILE *fp);
		char next_line(FILE fp);
		std::pair<std::string, std::string> get_pair(const std::string & a, const std::string & b);
		std::pair<std::string, std::string> get_pair(const std::string &a,
		const std::string &b);

		public:
		EIMPotentialFileReader(class LAMMPS* lmp, const std::string & filename);
		EIMPotentialFileReader(class LAMMPS* lmp, const std::string &filename,
		const int auto_convert=0);

		void get_global(PairEIM::Setfl *setfl);
		void get_element(PairEIM::Setfl *setfl, int i, const std::string &name);
		void get_pair(PairEIM::Setfl * setfl, int ij, const std::string & elemA, const std::string & elemB);
		void get_pair(PairEIM::Setfl *setfl, int ij,
		const std::string &elemA, const std::string &elemB);

		private:
		// potential parameters

src/MANYBODY/pair_gw.cpp

+12 −1

Original line number	Diff line number	Diff line
		@@ -48,6 +48,7 @@ PairGW::PairGW(LAMMPS *lmp) : Pair(lmp)
		restartinfo = 0;
		one_coeff = 1;
		manybody_flag = 1;
		unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);

		nelements = 0;
		elements = NULL;
		@@ -375,9 +376,14 @@ void PairGW::read_file(char *file)
		// open file on proc 0

		if (comm->me == 0) {
		PotentialFileReader reader(lmp, file, "GW");
		PotentialFileReader reader(lmp, file, "GW", unit_convert_flag);
		char * line;

		// transparently convert units for supported conversions

		int unit_convert = reader.get_unit_convert();
		double conversion_factor = utils::get_conversion_factor(utils::ENERGY,
		unit_convert);
		while((line = reader.next_line(NPARAMS_PER_LINE))) {
		try {
		ValueTokenizer values(line);
		@@ -427,6 +433,11 @@ void PairGW::read_file(char *file)
		params[nparams].lam1 = values.next_double();
		params[nparams].biga = values.next_double();
		params[nparams].powermint = int(params[nparams].powerm);

		if (unit_convert) {
		params[nparams].biga *= conversion_factor;
		params[nparams].bigb *= conversion_factor;
		}
		} catch (TokenizerException & e) {
		error->one(FLERR, e.what());
		}

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