forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@156 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
ff281681e3
commit
8d472f2113
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "stdlib.h"
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#include "lattice.h"
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#include "update.h"
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#include "force.h"
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#include "comm.h"
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#include "memory.h"
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#include "error.h"
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#define MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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#define BIG 1.0e30
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enum {NONE,SC,BCC,FCC,DIAMOND,SQ,SQ2,HEX,USER};
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/* ---------------------------------------------------------------------- */
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Lattice::Lattice(int narg, char **arg)
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{
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// parse style arg
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if (narg < 1) error->all("Illegal lattice command");
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if (strcmp(arg[0],"none") == 0) style = NONE;
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else if (strcmp(arg[0],"sc") == 0) style = SC;
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else if (strcmp(arg[0],"bcc") == 0) style = BCC;
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else if (strcmp(arg[0],"fcc") == 0) style = FCC;
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else if (strcmp(arg[0],"diamond") == 0) style = DIAMOND;
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else if (strcmp(arg[0],"sq") == 0) style = SQ;
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else if (strcmp(arg[0],"sq2") == 0) style = SQ2;
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else if (strcmp(arg[0],"hex") == 0) style = HEX;
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else if (strcmp(arg[0],"user") == 0) style = USER;
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else error->all("Illegal lattice command");
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if (style == NONE) {
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if (narg > 1) error->all("Illegal lattice command");
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return;
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}
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// check that lattice matches dimension
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// style USER can be either 2d or 3d
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int dimension = force->dimension;
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if (dimension == 2) {
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if (style == SC || style == BCC || style == FCC || style == DIAMOND)
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error->all("Lattice style incompatible with simulation dimension");
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}
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if (dimension == 3) {
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if (style == SQ || style == SQ2 || style == HEX)
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error->all("Lattice style incompatible with simulation dimension");
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}
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// scale = conversion factor between lattice and box units
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if (narg < 2) error->all("Illegal lattice command");
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scale = atof(arg[1]);
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if (scale <= 0.0) error->all("Illegal lattice command");
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// set basis atoms for each style
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// x,y,z = fractional coords within unit cell
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// style USER will be defined by optional args
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nbasis = 0;
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basis = NULL;
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if (style == SC) {
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add_basis(0.0,0.0,0.0);
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} else if (style == BCC) {
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add_basis(0.0,0.0,0.0);
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add_basis(0.5,0.5,0.5);
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} else if (style == FCC) {
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add_basis(0.0,0.0,0.0);
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add_basis(0.5,0.5,0.0);
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add_basis(0.5,0.0,0.5);
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add_basis(0.0,0.5,0.5);
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} else if (style == SQ) {
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add_basis(0.0,0.0,0.0);
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} else if (style == SQ2) {
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add_basis(0.0,0.0,0.0);
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add_basis(0.5,0.5,0.0);
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} else if (style == HEX) {
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add_basis(0.0,0.0,0.0);
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add_basis(0.5,0.5,0.0);
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} else if (style == DIAMOND) {
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add_basis(0.0,0.0,0.0);
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add_basis(0.0,0.5,0.5);
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add_basis(0.5,0.0,0.5);
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add_basis(0.5,0.5,0.0);
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add_basis(0.25,0.25,0.25);
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add_basis(0.25,0.75,0.75);
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add_basis(0.75,0.25,0.75);
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add_basis(0.75,0.75,0.25);
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}
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// set defaults for optional args
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origin[0] = origin[1] = origin[2] = 0.0;
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orientx[0] = 1; orientx[1] = 0; orientx[2] = 0;
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orienty[0] = 0; orienty[1] = 1; orienty[2] = 0;
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orientz[0] = 0; orientz[1] = 0; orientz[2] = 1;
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a1[0] = 1.0; a1[1] = 0.0; a1[2] = 0.0;
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a2[0] = 0.0; a2[1] = 1.0; a2[2] = 0.0;
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a3[0] = 0.0; a3[1] = 0.0; a3[2] = 1.0;
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if (style == HEX) a2[1] = sqrt(3.0);
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// process optional args
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int iarg = 2;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"origin") == 0) {
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if (iarg+4 > narg) error->all("Illegal lattice command");
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origin[0] = atof(arg[iarg+1]);
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origin[1] = atof(arg[iarg+2]);
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origin[2] = atof(arg[iarg+3]);
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if (origin[0] < 0.0 || origin[0] >= 1.0 ||
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origin[1] < 0.0 || origin[1] >= 1.0 ||
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origin[2] < 0.0 || origin[2] >= 1.0)
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error->all("Illegal lattice command");
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iarg += 4;
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} else if (strcmp(arg[iarg],"orient") == 0) {
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if (iarg+5 > narg) error->all("Illegal lattice command");
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int dim;
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if (strcmp(arg[iarg+1],"x") == 0) dim = 0;
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else if (strcmp(arg[iarg+1],"y") == 0) dim = 1;
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else if (strcmp(arg[iarg+1],"z") == 0) dim = 2;
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else error->all("Illegal lattice command");
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int *orient;
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if (dim == 0) orient = orientx;
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else if (dim == 1) orient = orienty;
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else if (dim == 2) orient = orientz;
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orient[0] = atoi(arg[iarg+2]);
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orient[1] = atoi(arg[iarg+3]);
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orient[2] = atoi(arg[iarg+4]);
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iarg += 5;
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} else if (strcmp(arg[iarg],"a1") == 0) {
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if (iarg+4 > narg) error->all("Illegal lattice command");
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if (style != USER)
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error->all("Invalid option in lattice command for non-user style");
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a1[0] = atof(arg[iarg+1]);
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a1[1] = atof(arg[iarg+2]);
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a1[2] = atof(arg[iarg+3]);
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iarg += 4;
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} else if (strcmp(arg[iarg],"a2") == 0) {
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if (iarg+4 > narg) error->all("Illegal lattice command");
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if (style != USER)
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error->all("Invalid option in lattice command for non-user style");
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a2[0] = atof(arg[iarg+1]);
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a2[1] = atof(arg[iarg+2]);
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a2[2] = atof(arg[iarg+3]);
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iarg += 4;
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} else if (strcmp(arg[iarg],"a3") == 0) {
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if (iarg+4 > narg) error->all("Illegal lattice command");
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if (style != USER)
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error->all("Invalid option in lattice command for non-user style");
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a3[0] = atof(arg[iarg+1]);
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a3[1] = atof(arg[iarg+2]);
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a3[2] = atof(arg[iarg+3]);
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iarg += 4;
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} else if (strcmp(arg[iarg],"basis") == 0) {
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if (iarg+4 > narg) error->all("Illegal lattice command");
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if (style != USER)
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error->all("Invalid option in lattice command for non-user style");
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double x = atof(arg[iarg+1]);
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double y = atof(arg[iarg+2]);
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double z = atof(arg[iarg+3]);
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if (x < 0.0 || x >= 1.0 || y < 0.0 || y >= 1.0 || z < 0.0 || z >= 1.0)
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error->all("Illegal lattice command");
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add_basis(x,y,z);
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iarg += 4;
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} else error->all("Illegal lattice command");
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}
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// check settings for errors
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if (nbasis == 0) error->all("No basis atoms in lattice");
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if (!orthogonal())
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error->all("Lattice orient vectors are not orthogonal");
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if (!right_handed())
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error->all("Lattice orient vectors are not right-handed");
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if (colinear())
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error->all("Lattice primitive vectors are colinear");
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if (dimension == 2) {
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if (origin[2] != 0.0)
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error->all("Lattice settings are not compatible with 2d simulation");
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if (orientx[2] != 0 || orienty[2] != 0 ||
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orientz[0] != 0 || orientz[1] != 0)
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error->all("Lattice settings are not compatible with 2d simulation");
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if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0)
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error->all("Lattice settings are not compatible with 2d simulation");
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}
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// reset scale for LJ units (input scale is rho*)
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// scale = (Nbasis/(Vprimitive * rho*)) ^ (1/dim)
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if (strcmp(update->unit_style,"lj") == 0) {
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double vec[3];
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cross(a2,a3,vec);
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double volume = dot(a1,vec);
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scale = pow(nbasis/volume/scale,1.0/dimension);
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}
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// initialize lattice <-> box transformation matrices
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setup_transform();
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// convert 8 corners of primitive unit cell from lattice coords to box coords
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// min to max = bounding box around the pts in box space
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// xlattice,ylattice,zlattice = extent of bbox in box space
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// set xlattice,ylattice,zlattice to 0.0 initially
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// since bbox uses them to shift origin (irrelevant for this computation)
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double xmin,ymin,zmin,xmax,ymax,zmax;
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xmin = ymin = zmin = BIG;
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xmax = ymax = zmax = -BIG;
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xlattice = ylattice = zlattice = 0.0;
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bbox(0,0.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax);
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bbox(0,1.0,0.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax);
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bbox(0,0.0,1.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax);
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bbox(0,1.0,1.0,0.0,xmin,ymin,zmin,xmax,ymax,zmax);
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bbox(0,0.0,0.0,1.0,xmin,ymin,zmin,xmax,ymax,zmax);
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bbox(0,1.0,0.0,1.0,xmin,ymin,zmin,xmax,ymax,zmax);
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bbox(0,0.0,1.0,1.0,xmin,ymin,zmin,xmax,ymax,zmax);
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bbox(0,1.0,1.0,1.0,xmin,ymin,zmin,xmax,ymax,zmax);
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xlattice = xmax - xmin;
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ylattice = ymax - ymin;
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zlattice = zmax - zmin;
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// print lattice spacings
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if (comm->me == 0) {
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if (screen)
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fprintf(screen,"Lattice spacing in x,y,z = %g %g %g\n",
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xlattice,ylattice,zlattice);
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if (logfile)
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fprintf(logfile,"Lattice spacing in x,y,z = %g %g %g\n",
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xlattice,ylattice,zlattice);
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}
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}
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/* ---------------------------------------------------------------------- */
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Lattice::~Lattice()
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{
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memory->destroy_2d_double_array(basis);
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}
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/* ----------------------------------------------------------------------
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check if 3 orientation vectors are mutually orthogonal
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------------------------------------------------------------------------- */
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int Lattice::orthogonal()
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{
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if (orientx[0]*orienty[0] + orientx[1]*orienty[1] +
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orientx[2]*orienty[2]) return 0;
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if (orienty[0]*orientz[0] + orienty[1]*orientz[1] +
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orienty[2]*orientz[2]) return 0;
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if (orientx[0]*orientz[0] + orientx[1]*orientz[1] +
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orientx[2]*orientz[2]) return 0;
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return 1;
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}
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/* ----------------------------------------------------------------------
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check righthandedness of orientation vectors
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x cross y must be in same direction as z
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------------------------------------------------------------------------- */
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int Lattice::right_handed()
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{
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int xy0 = orientx[1]*orienty[2] - orientx[2]*orienty[1];
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int xy1 = orientx[2]*orienty[0] - orientx[0]*orienty[2];
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int xy2 = orientx[0]*orienty[1] - orientx[1]*orienty[0];
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if (xy0*orientz[0] + xy1*orientz[1] + xy2*orientz[2] <= 0) return 0;
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return 1;
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}
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/* ----------------------------------------------------------------------
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check colinearity of each pair of primitive vectors
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------------------------------------------------------------------------- */
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int Lattice::colinear()
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{
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double vec[3];
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cross(a1,a2,vec);
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if (dot(vec,vec) == 0.0) return 1;
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cross(a2,a3,vec);
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if (dot(vec,vec) == 0.0) return 1;
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cross(a1,a3,vec);
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if (dot(vec,vec) == 0.0) return 1;
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return 0;
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}
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/* ----------------------------------------------------------------------
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initialize lattice <-> box transformation matrices
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------------------------------------------------------------------------- */
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void Lattice::setup_transform()
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{
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double length;
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// primitive = 3x3 matrix with primitive vectors as columns
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primitive[0][0] = a1[0];
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primitive[1][0] = a1[1];
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primitive[2][0] = a1[2];
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primitive[0][1] = a2[0];
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primitive[1][1] = a2[1];
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primitive[2][1] = a2[2];
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primitive[0][2] = a3[0];
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primitive[1][2] = a3[1];
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primitive[2][2] = a3[2];
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// priminv = inverse of primitive
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double determinant = primitive[0][0]*primitive[1][1]*primitive[2][2] +
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primitive[0][1]*primitive[1][2]*primitive[2][0] +
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primitive[0][2]*primitive[1][0]*primitive[2][1] -
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primitive[0][0]*primitive[1][2]*primitive[2][1] -
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primitive[0][1]*primitive[1][0]*primitive[2][2] -
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primitive[0][2]*primitive[1][1]*primitive[2][0];
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if (determinant == 0.0) error->all("Degenerate lattice primitive vectors");
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priminv[0][0] = (primitive[1][1]*primitive[2][2] -
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primitive[1][2]*primitive[2][1]) / determinant;
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priminv[1][0] = (primitive[1][2]*primitive[2][0] -
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primitive[1][0]*primitive[2][2]) / determinant;
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priminv[2][0] = (primitive[1][0]*primitive[2][1] -
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primitive[1][1]*primitive[2][0]) / determinant;
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priminv[0][1] = (primitive[0][2]*primitive[2][1] -
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primitive[0][1]*primitive[2][2]) / determinant;
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priminv[1][1] = (primitive[0][0]*primitive[2][2] -
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primitive[0][2]*primitive[2][0]) / determinant;
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priminv[2][1] = (primitive[0][1]*primitive[2][0] -
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primitive[0][0]*primitive[2][1]) / determinant;
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priminv[0][2] = (primitive[0][1]*primitive[1][2] -
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primitive[0][2]*primitive[1][1]) / determinant;
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priminv[1][2] = (primitive[0][2]*primitive[1][0] -
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primitive[0][0]*primitive[1][2]) / determinant;
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priminv[2][2] = (primitive[0][0]*primitive[1][1] -
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primitive[0][1]*primitive[1][0]) / determinant;
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// rotaterow = 3x3 matrix with normalized orient vectors as rows
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length = sqrt(orientx[0]*orientx[0] + orientx[1]*orientx[1] +
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orientx[2]*orientx[2]);
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if (length == 0.0) error->all("Zero-length lattice orient vector");
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rotaterow[0][0] = orientx[0] / length;
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rotaterow[0][1] = orientx[1] / length;
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rotaterow[0][2] = orientx[2] / length;
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length = sqrt(orienty[0]*orienty[0] + orienty[1]*orienty[1] +
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orienty[2]*orienty[2]);
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if (length == 0.0) error->all("Zero-length lattice orient vector");
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rotaterow[1][0] = orienty[0] / length;
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rotaterow[1][1] = orienty[1] / length;
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rotaterow[1][2] = orienty[2] / length;
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length = sqrt(orientz[0]*orientz[0] + orientz[1]*orientz[1] +
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orientz[2]*orientz[2]);
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if (length == 0.0) error->all("Zero-length lattice orient vector");
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rotaterow[2][0] = orientz[0] / length;
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rotaterow[2][1] = orientz[1] / length;
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rotaterow[2][2] = orientz[2] / length;
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// rotatecol = 3x3 matrix with normalized orient vectors as columns
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rotatecol[0][0] = rotaterow[0][0];
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rotatecol[1][0] = rotaterow[0][1];
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rotatecol[2][0] = rotaterow[0][2];
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rotatecol[0][1] = rotaterow[1][0];
|
||||
rotatecol[1][1] = rotaterow[1][1];
|
||||
rotatecol[2][1] = rotaterow[1][2];
|
||||
|
||||
rotatecol[0][2] = rotaterow[2][0];
|
||||
rotatecol[1][2] = rotaterow[2][1];
|
||||
rotatecol[2][2] = rotaterow[2][2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert lattice coords to box coords
|
||||
input x,y,z = point in lattice coords
|
||||
output x,y,z = point in box coords
|
||||
transformation: xyz_box = Rotate_row * scale * P * xyz_lattice + offset
|
||||
xyz_box = 3-vector of output box coords
|
||||
Rotate_row = 3x3 matrix = normalized orient vectors as rows
|
||||
scale = scale factor
|
||||
P = 3x3 matrix = primitive vectors as columns
|
||||
xyz_lattice = 3-vector of input lattice coords
|
||||
offset = 3-vector = (xlatt*origin[0], ylatt*origin[1], zlatt*origin[2])
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Lattice::lattice2box(double &x, double &y, double &z)
|
||||
{
|
||||
double x1 = primitive[0][0]*x + primitive[0][1]*y + primitive[0][2]*z;
|
||||
double y1 = primitive[1][0]*x + primitive[1][1]*y + primitive[1][2]*z;
|
||||
double z1 = primitive[2][0]*x + primitive[2][1]*y + primitive[2][2]*z;
|
||||
|
||||
x1 *= scale;
|
||||
y1 *= scale;
|
||||
z1 *= scale;
|
||||
|
||||
double xnew = rotaterow[0][0]*x1 + rotaterow[0][1]*y1 + rotaterow[0][2]*z1;
|
||||
double ynew = rotaterow[1][0]*x1 + rotaterow[1][1]*y1 + rotaterow[1][2]*z1;
|
||||
double znew = rotaterow[2][0]*x1 + rotaterow[2][1]*y1 + rotaterow[2][2]*z1;
|
||||
|
||||
x = xnew + xlattice*origin[0];
|
||||
y = ynew + ylattice*origin[1];
|
||||
z = znew + zlattice*origin[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert box coords to lattice coords
|
||||
input x,y,z = point in box coords
|
||||
output x,y,z = point in lattice coords
|
||||
transformation: xyz_latt = P_inv * 1/scale * Rotate_col * (xyz_box - offset)
|
||||
xyz_lattice = 3-vector of output lattice coords
|
||||
P_inv = 3x3 matrix = inverse of primitive vectors as columns
|
||||
scale = scale factor
|
||||
Rotate_col = 3x3 matrix = normalized orient vectors as columns
|
||||
xyz_box = 3-vector of input box coords
|
||||
offset = 3-vector = (xlatt*origin[0], ylatt*origin[1], zlatt*origin[2])
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Lattice::box2lattice(double &x, double &y, double &z)
|
||||
{
|
||||
x -= xlattice*origin[0];
|
||||
y -= ylattice*origin[1];
|
||||
z -= zlattice*origin[2];
|
||||
|
||||
double x1 = rotatecol[0][0]*x + rotatecol[0][1]*y + rotatecol[0][2]*z;
|
||||
double y1 = rotatecol[1][0]*x + rotatecol[1][1]*y + rotatecol[1][2]*z;
|
||||
double z1 = rotatecol[2][0]*x + rotatecol[2][1]*y + rotatecol[2][2]*z;
|
||||
|
||||
x1 /= scale;
|
||||
y1 /= scale;
|
||||
z1 /= scale;
|
||||
|
||||
x = priminv[0][0]*x1 + priminv[0][1]*y1 + priminv[0][2]*z1;
|
||||
y = priminv[1][0]*x1 + priminv[1][1]*y1 + priminv[1][2]*z1;
|
||||
z = priminv[2][0]*x1 + priminv[2][1]*y1 + priminv[2][2]*z1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add a basis atom to list
|
||||
x,y,z = fractional coords within unit cell
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Lattice::add_basis(double x, double y, double z)
|
||||
{
|
||||
basis = memory->grow_2d_double_array(basis,nbasis+1,3,"lattice:basis");
|
||||
basis[nbasis][0] = x;
|
||||
basis[nbasis][1] = y;
|
||||
basis[nbasis][2] = z;
|
||||
nbasis++;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return x dot y
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double Lattice::dot(double *x, double *y)
|
||||
{
|
||||
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
z = x cross y
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Lattice::cross(double *x, double *y, double *z)
|
||||
{
|
||||
z[0] = x[1]*y[2] - x[2]*y[1];
|
||||
z[1] = x[2]*y[0] - x[0]*y[2];
|
||||
z[2] = x[0]*y[1] - x[1]*y[0];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert x,y,z from lattice coords to box coords (flag = 0) or vice versa
|
||||
use new point to expand bounding box (min to max)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Lattice::bbox(int flag, double x, double y, double z,
|
||||
double &xmin, double &ymin, double &zmin,
|
||||
double &xmax, double &ymax, double &zmax)
|
||||
{
|
||||
if (flag == 0) lattice2box(x,y,z);
|
||||
else box2lattice(x,y,z);
|
||||
|
||||
xmin = MIN(x,xmin); ymin = MIN(y,ymin); zmin = MIN(z,zmin);
|
||||
xmax = MAX(x,xmax); ymax = MAX(y,ymax); zmax = MAX(z,zmax);
|
||||
}
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LATTICE_H
|
||||
#define LATTICE_H
|
||||
|
||||
#include "lammps.h"
|
||||
|
||||
class Lattice : public LAMMPS {
|
||||
public:
|
||||
int style; // enum list of NONE,SC,FCC,etc
|
||||
double xlattice,ylattice,zlattice; // lattice scale factors in 3 dims
|
||||
int nbasis; // # of atoms in basis of unit cell
|
||||
double **basis; // fractional coords of each basis atom
|
||||
// within unit cell (0 <= coord < 1)
|
||||
Lattice(int, char **);
|
||||
~Lattice();
|
||||
void lattice2box(double &, double &, double &);
|
||||
void box2lattice(double &, double &, double &);
|
||||
void bbox(int, double, double, double,
|
||||
double &, double &, double &, double &, double &, double &);
|
||||
|
||||
private:
|
||||
double scale;
|
||||
double origin[3]; // lattice origin
|
||||
int orientx[3]; // lattice orientation vecs
|
||||
int orienty[3]; // orientx = what lattice dir lies
|
||||
int orientz[3]; // along x dim in box
|
||||
double a1[3],a2[3],a3[3]; // vectors that bound unit cell
|
||||
|
||||
double primitive[3][3]; // lattice <-> box transform matrices
|
||||
double priminv[3][3];
|
||||
double rotaterow[3][3];
|
||||
double rotatecol[3][3];
|
||||
|
||||
int orthogonal();
|
||||
int right_handed();
|
||||
int colinear();
|
||||
void setup_transform();
|
||||
void add_basis(double, double, double);
|
||||
double dot(double *, double *);
|
||||
void cross(double *, double *, double *);
|
||||
};
|
||||
|
||||
#endif
|
||||
Loading…
Reference in New Issue