LammpsInterface.cpp
0977af1299aalammm-master

LammpsInterface.cpp
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			// Header file for this class
			#include "LammpsInterface.h"

			// LAMMPS includes
			#include "lammps.h"
			#include "atom.h" // x, v, f
			#include "domain.h" // for basing locations on regions
			#include "region.h" // region bounding box and style
			#include "force.h" // boltzman constant
			#include "group.h" // atom masks
			#include "memory.h" // grow atom information
			#include "compute.h" // computes
			#include "modify.h" //
			#include "neighbor.h" // neighbors
			#include "neigh_list.h" // neighbor list
			#include "update.h" // timestepping information
			#include "pair.h" // pair potentials
			#include "lattice.h" // lattice parameters
			#include "comm.h" //

			// ATC includes
			#include "ATC_Error.h"
			#include "MatrixLibrary.h"

			// Other include files
			#include "mpi.h"
			#include <cstring>

			namespace ATC {


			LammpsInterface * LammpsInterface::myInstance_ = NULL;

			// -----------------------------------------------------------------
			// instance()
			// -----------------------------------------------------------------
			LammpsInterface * LammpsInterface::instance()
			{
			if (myInstance_ == NULL) {
			myInstance_ = new LammpsInterface();
			}
			return myInstance_;
			}

			// -----------------------------------------------------------------
			// constructor
			// -----------------------------------------------------------------
			LammpsInterface::LammpsInterface()
			: lammps_(NULL),
			atomPE_(NULL),
			commRank_(0)
			{
			}

			// -----------------------------------------------------------------
			// general interface methods
			// -----------------------------------------------------------------

			MPI_Comm LammpsInterface::world() { return lammps_->world; }

			// -----------------------------------------------------------------
			// atom interface methods
			// -----------------------------------------------------------------

			int LammpsInterface::nlocal() { return lammps_->atom->nlocal; }

			int LammpsInterface::nghost() { return lammps_->atom->nghost; }

			double LammpsInterface::natoms() { return lammps_->atom->natoms; }

			int LammpsInterface::nmax() { return lammps_->atom->nmax; }

			int LammpsInterface::ntypes() { return lammps_->atom->ntypes; }

			double ** LammpsInterface::xatom() { return lammps_->atom->x; }

			const double LammpsInterface::xatom() const { return (const double)(lammps_->atom->x); }

			double ** LammpsInterface::vatom() { return lammps_->atom->v; }

			double ** LammpsInterface::fatom() { return lammps_->atom->f; }

			int * LammpsInterface::atom_mask() { return lammps_->atom->mask; }

			int * LammpsInterface::atom_type() { return lammps_->atom->type; }

			int * LammpsInterface::atom_tag() { return lammps_->atom->tag; }

			double * LammpsInterface::atom_mass() { return lammps_->atom->mass; }

			double LammpsInterface::atom_mass(int iType) { return lammps_->atom->mass[iType]; }

			double * LammpsInterface::atom_rmass() { return lammps_->atom->rmass; }

			double * LammpsInterface::atom_charge() { return lammps_->atom->q; }

			// -----------------------------------------------------------------
			// domain interface methods
			// -----------------------------------------------------------------

			int LammpsInterface::dimension() { return lammps_->domain->dimension; }

			int LammpsInterface::nregion() { return lammps_->domain->nregion; }

			void LammpsInterface::get_box_bounds(double & boxxlo, double & boxxhi,
			double & boxylo, double & boxyhi,
			double & boxzlo, double &boxzhi)
			{
			if (lammps_->domain->triclinic == 0) {
			boxxlo = lammps_->domain->boxlo[0];
			boxxhi = lammps_->domain->boxhi[0];
			boxylo = lammps_->domain->boxlo[1];
			boxyhi = lammps_->domain->boxhi[1];
			boxzlo = lammps_->domain->boxlo[2];
			boxzhi = lammps_->domain->boxhi[2];
			}
			else {
			boxxlo = lammps_->domain->boxlo_bound[0];
			boxxhi = lammps_->domain->boxhi_bound[0];
			boxylo = lammps_->domain->boxlo_bound[1];
			boxyhi = lammps_->domain->boxhi_bound[1];
			boxzlo = lammps_->domain->boxlo_bound[2];
			boxzhi = lammps_->domain->boxhi_bound[2];
			}
			}

			int LammpsInterface::xperiodic() { return lammps_->domain->xperiodic; }

			int LammpsInterface::yperiodic() { return lammps_->domain->yperiodic; }

			int LammpsInterface::zperiodic() { return lammps_->domain->zperiodic; }

			int LammpsInterface::nperiodic()
			{
			int nprd = 0;
			if ( lammps_->domain->xperiodic > 0 ) { nprd++ ; }
			if ( lammps_->domain->yperiodic > 0 ) { nprd++ ; }
			if ( lammps_->domain->zperiodic > 0 ) { nprd++ ; }
			return nprd;
			}

			double LammpsInterface::domain_xprd() { return lammps_->domain->xprd; }

			double LammpsInterface::domain_yprd() { return lammps_->domain->yprd; }

			double LammpsInterface::domain_zprd() { return lammps_->domain->zprd; }

			double LammpsInterface::domain_xy() { return lammps_->domain->xy; }

			double LammpsInterface::domain_xz() { return lammps_->domain->xz; }

			double LammpsInterface::domain_yz() { return lammps_->domain->yz; }

			int LammpsInterface::domain_triclinic() { return lammps_->domain->triclinic; }

			void LammpsInterface::get_box_periodicity(int & xperiodic,
			int & yperiodic,
			int & zperiodic)
			{
			xperiodic = lammps_->domain->xperiodic;
			yperiodic = lammps_->domain->yperiodic;
			zperiodic = lammps_->domain->zperiodic;
			}

			int LammpsInterface::get_region_id(const char * regionName) {
			int nregion = this->nregion();
			for (int iregion = 0; iregion < nregion; iregion++) {
			if (strcmp(regionName, region_name(iregion)) == 0) {
			return iregion;
			}
			}
			throw ATC_Error(0,"Region has not been defined");
			return -1;
			}
			// -----------------------------------------------------------------
			// update interface methods
			// -----------------------------------------------------------------
			LammpsInterface::UnitsType LammpsInterface::units_style(void)
			{
			if (strcmp(lammps_->update->unit_style,"lj") == 0) return LJ;
			else if (strcmp(lammps_->update->unit_style,"real") == 0) return REAL;
			else if (strcmp(lammps_->update->unit_style,"metal") == 0) return METAL;
			else return UNKNOWN;
			}


			// -----------------------------------------------------------------
			// lattice interface methods
			// -----------------------------------------------------------------

			double LammpsInterface::xlattice() { return lammps_->domain->lattice->xlattice; }

			double LammpsInterface::ylattice() { return lammps_->domain->lattice->ylattice; }

			double LammpsInterface::zlattice() { return lammps_->domain->lattice->zlattice; }

			LammpsInterface::LatticeType LammpsInterface::lattice_style()
			{
			if (lammps_->domain->lattice)
			return (LammpsInterface::LatticeType)lammps_->domain->lattice->style;
			else
			throw ATC_Error(0,"Lattice has not been defined");
			}

			//* retuns the number of basis vectors
			int LammpsInterface::get_n_basis()
			{
			return lammps_->domain->lattice->nbasis;
			}

			//* returns the basis vectors, transformed to the box coords
			void LammpsInterface::get_basis(double **basis)
			{
			LAMMPS_NS::Lattice *lattice = lammps_->domain->lattice;
			int i,j;
			double origin[3] = {0.0, 0.0, 0.0};
			lattice->lattice2box(origin[0], origin[1], origin[2]);
			for (i=0; i<get_n_basis(); i++)
			{
			memcpy(basis[i],lattice->basis[i],3*sizeof(double));
			lattice->lattice2box(basis[i][0], basis[i][1], basis[i][2]);
			for (j=0; j<3; j++) basis[i][j] -= origin[j];
			}
			}

			//* gets the unit cell vectors
			void LammpsInterface::get_unit_cell(double a1, double a2, double *a3)
			{
			int i, j;
			double *a[3] = {a1,a2,a3};
			double origin[3] = {0.0,0.0,0.0};
			LAMMPS_NS::Lattice *lattice = lammps_->domain->lattice;
			// transform origin
			lattice->lattice2box(origin[0], origin[1], origin[2]);

			// copy reference lattice vectors
			memcpy(a[0], lattice->a1, 3*sizeof(double));
			memcpy(a[1], lattice->a2, 3*sizeof(double));
			memcpy(a[2], lattice->a3, 3*sizeof(double));

			for (i=0; i<3; i++)
			{
			lattice->lattice2box(a[i][0], a[i][1], a[i][2]);
			for (j=0; j<3; j++) a[i][j] -= origin[j];
			}
			}

			//* gets number of atoms in a unit cell
			int LammpsInterface::num_atoms_per_cell(void)
			{
			int naCell = 0;
			LatticeType type = lattice_style();
			if (type == LammpsInterface::SC) naCell = 1;
			else if (type == LammpsInterface::BCC) naCell = 2;
			else if (type == LammpsInterface::FCC) naCell = 4;
			else if (type == LammpsInterface::DIAMOND) naCell = 8;
			else if (comm_rank()==0) {
			//{throw ATC_Error(0,"lattice style not currently supported by ATC");}
			cout << "ATC WARNING: Cannot get number of atoms per cell from lattice\n";
			naCell = 1; //HACK to enable us to keep going since this is only used to compute volume per atom
			// ATC modes with a user specified atomic volume or using only volumetric quantities are fine
			}
			return naCell;
			}

			//* gets tributary volume for an atom
			double LammpsInterface::volume_per_atom(void)
			{
			double naCell = num_atoms_per_cell();
			double volPerAtom =
			xlattice() * ylattice() * zlattice() / naCell;
			return volPerAtom;
			}

			//* gets lattice basis
			void LammpsInterface::get_lattice(MATRIX &N, MATRIX &B)
			{
			int nbasis = get_n_basis();
			double *basis = new double[nbasis];
			N.reset(3,3);
			B.reset(3,nbasis);
			for (int i=0; i<nbasis; i++) basis[i] = column(B,i).get_ptr();
			get_basis(basis);
			get_unit_cell(column(N,0).get_ptr(),
			column(N,1).get_ptr(),
			column(N,2).get_ptr());
			delete [] basis;
			}


			// -----------------------------------------------------------------
			// force interface methods
			// -----------------------------------------------------------------

			double LammpsInterface::boltz() { return lammps_->force->boltz; }

			double LammpsInterface::mvv2e() { return lammps_->force->mvv2e; }

			double LammpsInterface::ftm2v() { return lammps_->force->ftm2v; }

			double LammpsInterface::nktv2p() { return lammps_->force->nktv2p; }

			double LammpsInterface::qqr2e() { return lammps_->force->qqr2e; }

			double LammpsInterface::qe2f() { return lammps_->force->qe2f; }

			double LammpsInterface::dielectric() { return lammps_->force->dielectric; }

			double LammpsInterface::qqrd2e() { return lammps_->force->qqrd2e; }

			double LammpsInterface::pair_force(int i, int j, double rsq,
			double & fmag_over_rmag)
			{
			int itype = (lammps_->atom->type)[i];
			int jtype = (lammps_->atom->type)[j];
			// return value is the energy
			if (rsq < (lammps_->force->pair->cutsq)[itype][jtype]) {
			return lammps_->force->pair->single(i,j,itype,jtype,
			rsq,1.0,1.0,fmag_over_rmag);
			}
			return 0.0;
			}

			double LammpsInterface::pair_cutoff()
			{
			return lammps_->force->pair->cutforce;
			}

			int LammpsInterface::single_enable()
			{
			return lammps_->force->pair->single_enable;
			}

			//* Boltzmann's constant in M,L,T,t units
			double LammpsInterface::kBoltzmann() {
			return (lammps_->force->boltz)/(lammps_->force->mvv2e);
			}

			//* Dulong-Petit heat capacity
			double LammpsInterface::heat_capacity() {
			double rhoCp = dimension()*kBoltzmann()/volume_per_atom();
			return rhoCp;
			}

			//* reference mass density
			double LammpsInterface::mass_density()
			{
			const int ntypes = lammps_->atom->ntypes;
			const int *mass_setflag = lammps_->atom->mass_setflag;
			const int *type = lammps_->atom->type;
			const double *mass = lammps_->atom->mass;
			const double *rmass = lammps_->atom->rmass;
			// NOTE currently assumes all atoms have same mass and volume
			// in the future, mass and volume will be different but density should be
			// an atom indepedent quantity
			if (mass) {
			if (type) return mass[type[0]]/volume_per_atom();
			// no type array - just use first type that has a set mass
			for (int i=1; i<=ntypes; i++) {
			if (mass_setflag[i]) return mass[i]/volume_per_atom();
			}
			// NOTE: no masses specified in input file should we warn the user of this?
			return 0.0;
			}
			// NOTE is this valid - lammps likes to not use 0 index
			if (rmass) return rmass[0]/volume_per_atom();
			return 0.0;
			}

			// -----------------------------------------------------------------
			// group interface methods
			// -----------------------------------------------------------------

			int LammpsInterface::ngroup() { return lammps_->group->ngroup; }

			int LammpsInterface::group_bit(int iGroup) { return lammps_->group->bitmask[iGroup]; }

			int LammpsInterface::find_group(const char * c) { return lammps_->group->find(c); }

			int LammpsInterface::group_inverse_mask(int iGroup)
			{
			return lammps_->group->inversemask[iGroup];
			}

			char * LammpsInterface::group_name(int iGroup)
			{
			return lammps_->group->names[iGroup];
			}

			void LammpsInterface::group_bounds(int iGroup, double * b)
			{
			lammps_->group->bounds(iGroup, b);
			}


			// -----------------------------------------------------------------
			// memory interface methods
			// -----------------------------------------------------------------

			double * LammpsInterface::create_1d_double_array(int nlo, int nhi, const char *name) {
			double *array;
			return lammps_->memory->create1d_offset(array, nlo, nhi, name);
			}

			void LammpsInterface::destroy_1d_double_array(double * d, int i) {
			lammps_->memory->destroy1d_offset(d, i);
			}

			double ** LammpsInterface::create_2d_double_array(int n1, int n2, const char *name) {
			double **array;
			return lammps_->memory->create(array, n1, n2, name);
			}

			void LammpsInterface::destroy_2d_double_array(double **d) {
			lammps_->memory->destroy(d);
			}

			double LammpsInterface::grow_2d_double_array(double array,
			int n1,
			int n2,
			const char *name)
			{
			return lammps_->memory->grow(array, n1, n2, name);
			}

			int ** LammpsInterface::create_2d_int_array(int n1, int n2, const char *name) {
			int **array;
			return lammps_->memory->create(array, n1, n2, name);
			}

			void LammpsInterface::destroy_2d_int_array(int **i) {
			lammps_->memory->destroy(i);
			}

			int LammpsInterface::grow_2d_int_array(int array, int n1, int n2, const char *name) {
			return lammps_->memory->grow(array, n1, n2, name);
			}


			// -----------------------------------------------------------------
			// update interface methods
			// -----------------------------------------------------------------

			double LammpsInterface::dt() { return lammps_->update->dt; }

			int LammpsInterface::ntimestep() { return lammps_->update->ntimestep; }

			int LammpsInterface::nsteps() { return lammps_->update->nsteps; }


			// -----------------------------------------------------------------
			// neighbor list interface methods
			// -----------------------------------------------------------------

			void LammpsInterface::init_list(int id, LAMMPS_NS::NeighList *ptr) { list_ = ptr; }

			int LammpsInterface::neighbor_list_inum() { return list_->inum; }

			int * LammpsInterface::neighbor_list_numneigh() { return list_->numneigh; }

			int * LammpsInterface::neighbor_list_ilist() { return list_->ilist; }

			int ** LammpsInterface::neighbor_list_firstneigh() { return list_->firstneigh; }

			int LammpsInterface::neighbor_ago() { return lammps_->neighbor->ago; }

			// -----------------------------------------------------------------
			// region interface methods
			// -----------------------------------------------------------------

			char * LammpsInterface::region_name(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->id;
			}

			char * LammpsInterface::region_style(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->style;
			}

			double LammpsInterface::region_xlo(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->extent_xlo;
			}

			double LammpsInterface::region_xhi(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->extent_xhi;
			}

			double LammpsInterface::region_ylo(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->extent_ylo;
			}

			double LammpsInterface::region_yhi(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->extent_yhi;
			}

			double LammpsInterface::region_zlo(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->extent_zlo;
			}

			double LammpsInterface::region_zhi(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->extent_zhi;
			}

			double LammpsInterface::region_xscale(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->xscale;
			}

			double LammpsInterface::region_yscale(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->yscale;
			}

			double LammpsInterface::region_zscale(int iRegion)
			{
			return lammps_->domain->regions[iRegion]->zscale;
			}

			int LammpsInterface::region_match(int iRegion, double x, double y, double z) {
			return lammps_->domain->regions[iRegion]->match(x,y,z);
			}

			// -----------------------------------------------------------------
			// compute methods
			// -----------------------------------------------------------------
			int LammpsInterface::find_compute(const char* tag)
			{
			// a clunky way to safely get rid of the const
			int n = strlen(tag) + 1;
			char* tag_copy = new char[n];
			strcpy(tag_copy,tag);

			int icompute = lammps_->modify->find_compute(tag_copy);
			if (icompute < 0) {
			string msg("Could not find compute ");
			msg += tag;
			throw ATC_Error(0,msg);
			}
			return icompute;
			}

			LAMMPS_NS::Compute* LammpsInterface::get_compute(const char* tag)
			{
			int icompute = find_compute(tag);
			LAMMPS_NS::Compute* cmpt = lammps_->modify->compute[icompute];
			return cmpt;
			}

			double** LammpsInterface::compute_vector_data(const char* tag)
			{
			LAMMPS_NS::Compute* cmpt = get_compute(tag);
			if (!(cmpt->invoked_flag & INVOKED_PERATOM)) {
			cmpt->compute_peratom();
			cmpt->invoked_flag \|= INVOKED_PERATOM;
			}
			return cmpt->array_atom;
			}

			double* LammpsInterface::compute_scalar_data(const char* tag)
			{
			LAMMPS_NS::Compute* cmpt = get_compute(tag);
			if (!(cmpt->invoked_flag & INVOKED_PERATOM)) {
			cmpt->compute_peratom();
			cmpt->invoked_flag \|= INVOKED_PERATOM;
			}
			return cmpt->vector_atom;
			}

			int LammpsInterface::compute_ncols(const char* tag)
			{
			int icompute = find_compute(tag);
			int ncols = lammps_->modify->compute[icompute]->size_peratom_cols;
			if (ncols == 0) ncols = 1; // oddity of lammps, used as flag for scalar
			return ncols;
			}

			// -----------------------------------------------------------------
			// compute pe/atom interface methods
			// -----------------------------------------------------------------
			int LammpsInterface::atomPE_create(void)
			{
			//char * list[3] = {"atcPE","all","pe/atom"};
			char * list[4] = {"atcPE","all","pe/atom","pair"};
			int icompute = lammps_->modify->find_compute(list[0]);
			if (icompute < 0) {
			lammps_->modify->add_compute(3,list);
			icompute = lammps_->modify->find_compute(list[0]);
			}
			if (! atomPE_ ) {
			atomPE_ = lammps_->modify->compute[icompute];
			}
			return icompute;
			}

			void LammpsInterface::atomPE_init(void)
			{
			if (atomPE_) {
			atomPE_->init();
			}
			else {
			throw ATC_Error(0,"no atomPE compute");
			}
			}

			void LammpsInterface::atomPE_addstep(int step)
			{
			atomPE_->addstep(step);
			}

			double * LammpsInterface::atomPE_compute(void)
			{
			if (atomPE_) {
			atomPE_->compute_peratom();
			return atomPE_->vector_atom;
			}
			else {
			return NULL;
			}
			}

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

			void LammpsInterface::unwrap_coordinates(int iatom, double* xatom)
			{
			double **x = lammps_->atom->x;
			int *mask = lammps_->atom->mask;
			int *image = lammps_->atom->image;
			int nlocal = lammps_->atom->nlocal;

			double *h = lammps_->domain->h;
			double xprd = lammps_->domain->xprd;
			double yprd = lammps_->domain->yprd;
			double zprd = lammps_->domain->zprd;
			int xbox,ybox,zbox;

			// for triclinic, need to unwrap current atom coord via h matrix
			// NOTE: Using current box dimensions.
			if (lammps_->domain->triclinic == 0) {
			xbox = (image[iatom] & 1023) - 512;
			ybox = (image[iatom] >> 10 & 1023) - 512;
			zbox = (image[iatom] >> 20) - 512;
			xatom[0] = x[iatom][0] + xbox*xprd;
			xatom[1] = x[iatom][1] + ybox*yprd;
			xatom[2] = x[iatom][2] + zbox*zprd;
			} else {
			xbox = (image[iatom] & 1023) - 512;
			ybox = (image[iatom] >> 10 & 1023) - 512;
			zbox = (image[iatom] >> 20) - 512;
			xatom[0] = x[iatom][0] + h[0]xbox + h[5]ybox + h[4]*zbox;
			xatom[1] = x[iatom][1] + h[1]ybox + h[3]zbox;
			xatom[2] = x[iatom][2] + h[2]*zbox;
			}
			}


			// -----------------------------------------------------------------
			// other methods
			// -----------------------------------------------------------------

			/** Return lammps pointer -- only as a last resort! */
			LAMMPS_NS::LAMMPS * LammpsInterface::get_lammps_ptr() { return lammps_; }

			}

lammps/lib/atc/LammpsInterface.cpp0977af1299aalammm-master

LammpsInterface.cppView Options

lammps/lib/atc/LammpsInterface.cpp
0977af1299aalammm-master

LammpsInterface.cpp
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