Merge pull request #1798 from martok/meamc-dec19 (1be81096) · Commits · 郑智淋 / lammps

doc/src/pair_meamc.rst

+9 −2

Original line number	Diff line number	Diff line
		@@ -233,15 +233,20 @@ where
		Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
		by K (I<=J); default = 2.0
		lattce(I,J) = lattice structure of I-J reference structure:
		dia = diamond (interlaced fcc for alloy)
		fcc = face centered cubic
		bcc = body centered cubic
		hcp = hexagonal close-packed
		dim = dimer
		dia = diamond (interlaced fcc for alloy)
		dia3= diamond structure with primary 1NN and secondary 3NN interation
		b1 = rock salt (NaCl structure)
		hcp = hexagonal close-packed
		c11 = MoSi2 structure
		l12 = Cu3Au structure (lower case L, followed by 12)
		b2 = CsCl structure (interpenetrating simple cubic)
		ch4 = methane-like structure, only for binary system
		lin = linear structure (180 degree angle)
		zig = zigzag structure with a uniform angle
		tri = H2O-like structure that has an angle
		nn2(I,J) = turn on second-nearest neighbor MEAM formulation for
		I-J pair (see for example :ref:`(Lee) <Lee>`).
		0 = second-nearest neighbor formulation off
		@@ -254,6 +259,8 @@ where
		zbl(I,J) = blend the MEAM I-J pair potential with the ZBL potential for small
		atom separations :ref:`(ZBL) <ZBL>`
		default = 1
		theta(I,J) = angle between three atoms in line, zigzag, and trimer reference structures in degrees
		default = 180
		gsmooth_factor = factor determining the length of the G-function smoothing
		region; only significant for ibar=0 or ibar=4.
		99.0 = short smoothing region, sharp step

doc/txt/pair_meamc.txt

+2 −0

Original line number	Diff line number	Diff line
		@@ -139,6 +139,8 @@ potential parameters:

		lat = lattice structure of reference configuration
		z = number of nearest neighbors in the reference structure
		This field is only read for compatibility, the correct
		value is inferred from the lattice structure
		ielement = atomic number
		atwt = atomic weight
		alat = lattice constant of reference structure

src/USER-MEAMC/meam.h

+59 −10

Original line number	Diff line number	Diff line
		@@ -2,13 +2,15 @@
		#define LMP_MEAM_H

		#include <cmath>
		#include <cstring>
		#include "math_const.h"

		#define maxelt 5

		namespace LAMMPS_NS {
		class Memory;

		typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t;
		typedef enum { FCC, BCC, HCP, DIM, DIA, DIA3, B1, C11, L12, B2, CH4, LIN, ZIG, TRI } lattice_t;

		class MEAM
		{
		@@ -26,9 +28,7 @@ private:

		// Ec_meam = cohesive energy
		// re_meam = nearest-neighbor distance
		// Omega_meam = atomic volume
		// B_meam = bulk modulus
		// Z_meam = number of first neighbors for reference structure
		// ielt_meam = atomic number of element
		// A_meam = adjustable parameter
		// alpha_meam = sqrt(9OmegaB/Ec)
		@@ -64,8 +64,11 @@ private:
		// nr,dr = pair function discretization parameters
		// nrar,rdrar = spline coeff array parameters

		// theta = angle between three atoms in line, zigzag, and trimer reference structures
		// stheta_meam = sin(theta/2) in radian used in line, zigzag, and trimer reference structures
		// ctheta_meam = cos(theta/2) in radian used in line, zigzag, and trimer reference structures

		double Ec_meam[maxelt][maxelt], re_meam[maxelt][maxelt];
		double Omega_meam[maxelt], Z_meam[maxelt];
		double A_meam[maxelt], alpha_meam[maxelt][maxelt], rho0_meam[maxelt];
		double delta_meam[maxelt][maxelt];
		double beta0_meam[maxelt], beta1_meam[maxelt];
		@@ -108,6 +111,10 @@ public:
		int maxneigh;
		double scrfcn, dscrfcn, *fcpair;

		//angle for trimer, zigzag, line reference structures
		double stheta_meam[maxelt][maxelt];
		double ctheta_meam[maxelt][maxelt];

		protected:
		// meam_funcs.cpp

		@@ -191,9 +198,12 @@ protected:
		double embedding(const double A, const double Ec, const double rhobar, double& dF) const;
		static double erose(const double r, const double re, const double alpha, const double Ec, const double repuls, const double attrac, const int form);

		static void get_shpfcn(const lattice_t latt, double (&s)[3]);
		static int get_Zij(const lattice_t latt);
		static int get_Zij2(const lattice_t latt, const double cmin, const double cmax, double &a, double &S);
		static void get_shpfcn(const lattice_t latt, const double sthe, const double cthe, double (&s)[3]);

		static int get_Zij2(const lattice_t latt, const double cmin, const double cmax,
		const double sthe, double &a, double &S);
		static int get_Zij2_b2nn(const lattice_t latt, const double cmin, const double cmax, double &S);

		protected:
		void meam_checkindex(int, int, int, int, int);
		void getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** x, int numneigh,
		@@ -204,6 +214,7 @@ protected:
		void alloyparams();
		void compute_pair_meam();
		double phi_meam(double, int, int);
		const double phi_meam_series(const double scrn, const int Z1, const int Z2, const int a, const int b, const double r, const double arat);
		void compute_reference_density();
		void get_tavref(double, double, double, double, double, double, double, double, double, double,
		double, double, double, int, int, lattice_t);
		@@ -212,7 +223,41 @@ protected:
		void interpolate_meam(int);

		public:
		void meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt, double* alpha,
		//-----------------------------------------------------------------------------
		// convert lattice spec to lattice_t
		// only use single-element lattices if single=true
		// return false on failure
		// return true and set lat on success
		static bool str_to_lat(const char* str, bool single, lattice_t& lat)
		{
		if (strcmp(str,"fcc") == 0) lat = FCC;
		else if (strcmp(str,"bcc") == 0) lat = BCC;
		else if (strcmp(str,"hcp") == 0) lat = HCP;
		else if (strcmp(str,"dim") == 0) lat = DIM;
		else if (strcmp(str,"dia") == 0) lat = DIA;
		else if (strcmp(str,"dia3") == 0) lat = DIA3;
		else if (strcmp(str,"lin") == 0) lat = LIN;
		else if (strcmp(str,"zig") == 0) lat = ZIG;
		else if (strcmp(str,"tri") == 0) lat = TRI;
		else {
		if (single)
		return false;

		if (strcmp(str,"b1") == 0) lat = B1;
		else if (strcmp(str,"c11") == 0) lat = C11;
		else if (strcmp(str,"l12") == 0) lat = L12;
		else if (strcmp(str,"b2") == 0) lat = B2;
		else if (strcmp(str,"ch4") == 0) lat = CH4;
		else if (strcmp(str,"lin") == 0) lat =LIN;
		else if (strcmp(str,"zig") == 0) lat = ZIG;
		else if (strcmp(str,"tri") == 0) lat = TRI;
		else return false;
		}
		return true;
		}

		static int get_Zij(const lattice_t latt);
		void meam_setup_global(int nelt, lattice_t* lat, int* ielement, double* atwt, double* alpha,
		double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
		double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero,
		int* ibar);
		@@ -222,9 +267,9 @@ public:
		void meam_dens_init(int i, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
		int numneigh_full, int* firstneigh_full, int fnoffset);
		void meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double* eng_vdwl,
		double* eatom, int ntype, int* type, int* fmap, int& errorflag);
		double* eatom, int ntype, int* type, int* fmap, double** scale, int& errorflag);
		void meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl,
		double* eatom, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
		double* eatom, int ntype, int* type, int* fmap, double scale, double x, int numneigh, int* firstneigh,
		int numneigh_full, int* firstneigh_full, int fnoffset, double f, double vatom);
		};

		@@ -234,6 +279,10 @@ static inline bool iszero(const double f) {
		return fabs(f) < 1e-20;
		}

		static inline bool isone(const double f) {
		return fabs(f-1.0) < 1e-20;
		}

		// Helper functions

		static inline double fdiv_zero(const double n, const double d) {

src/USER-MEAMC/meam_dens_final.cpp

+8 −3

Original line number	Diff line number	Diff line
		@@ -4,18 +4,20 @@ using namespace LAMMPS_NS;

		void
		MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double* eng_vdwl,
		double* eatom, int /ntype/, int* type, int* fmap, int& errorflag)
		double* eatom, int /ntype/, int* type, int* fmap, double** scale, int& errorflag)
		{
		int i, elti;
		int m;
		double rhob, G, dG, Gbar, dGbar, gam, shp[3], Z;
		double denom, rho_bkgd, Fl;
		double scaleii;

		// Complete the calculation of density

		for (i = 0; i < nlocal; i++) {
		elti = fmap[type[i]];
		if (elti >= 0) {
		scaleii = scale[type[i]][type[i]];
		rho1[i] = 0.0;
		rho2[i] = -1.0 / 3.0 * arho2b[i] * arho2b[i];
		rho3[i] = 0.0;
		@@ -52,12 +54,14 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
		gamma[i] = gamma[i] / (rho0[i] * rho0[i]);
		}

		Z = this->Z_meam[elti];
		Z = get_Zij(this->lattce_meam[elti][elti]);

		G = G_gam(gamma[i], this->ibar_meam[elti], errorflag);
		if (errorflag != 0)
		return;
		get_shpfcn(this->lattce_meam[elti][elti], shp);

		get_shpfcn(this->lattce_meam[elti][elti], this->stheta_meam[elti][elti], this->ctheta_meam[elti][elti], shp);

		if (this->ibar_meam[elti] <= 0) {
		Gbar = 1.0;
		dGbar = 0.0;
		@@ -113,6 +117,7 @@ MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_
		Fl = embedding(this->A_meam[elti], this->Ec_meam[elti][elti], rhob, frhop[i]);

		if (eflag_either != 0) {
		Fl *= scaleii;
		if (eflag_global != 0) {
		eng_vdwl = eng_vdwl + Fl;
		}

src/USER-MEAMC/meam_dens_init.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -197,7 +197,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double**
		// Now compute derivatives
		dscrfcn[jn] = 0.0;
		sfcij = sij * fcij;
		if (!iszero(sfcij) && !iszero(sfcij - 1.0)) {
		if (!iszero(sfcij) && !isone(sfcij)) {
		for (kn = 0; kn < numneigh_full; kn++) {
		k = firstneigh_full[kn];
		if (k == j) continue;

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