git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
108
src/lattice.cpp
108
src/lattice.cpp
@ -5,7 +5,7 @@
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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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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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@ -61,7 +61,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
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int dimension = domain->dimension;
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if (dimension == 2) {
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if (style == SC || style == BCC || style == FCC || style == HCP ||
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style == DIAMOND)
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style == DIAMOND)
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error->all(FLERR,"Lattice style incompatible with simulation dimension");
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}
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if (dimension == 3) {
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@ -143,9 +143,9 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
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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(FLERR,"Illegal lattice command");
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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(FLERR,"Illegal lattice command");
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iarg += 4;
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} else if (strcmp(arg[iarg],"orient") == 0) {
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@ -174,27 +174,27 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
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} else if (strcmp(arg[iarg],"a1") == 0) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
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if (style != CUSTOM)
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error->all(FLERR,
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"Invalid option in lattice command for non-custom style");
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if (style != CUSTOM)
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error->all(FLERR,
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"Invalid option in lattice command for non-custom 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(FLERR,"Illegal lattice command");
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if (style != CUSTOM)
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error->all(FLERR,
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"Invalid option in lattice command for non-custom style");
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if (style != CUSTOM)
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error->all(FLERR,
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"Invalid option in lattice command for non-custom 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(FLERR,"Illegal lattice command");
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if (style != CUSTOM)
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error->all(FLERR,
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"Invalid option in lattice command for non-custom style");
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if (style != CUSTOM)
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error->all(FLERR,
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"Invalid option in lattice command for non-custom 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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@ -202,14 +202,14 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
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} else if (strcmp(arg[iarg],"basis") == 0) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
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if (style != CUSTOM)
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error->all(FLERR,
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"Invalid option in lattice command for non-custom style");
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if (style != CUSTOM)
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error->all(FLERR,
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"Invalid option in lattice command for non-custom 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(FLERR,"Illegal lattice command");
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error->all(FLERR,"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(FLERR,"Illegal lattice command");
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@ -228,14 +228,14 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
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if (dimension == 2) {
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if (origin[2] != 0.0)
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error->all(FLERR,
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"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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"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(FLERR,
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"Lattice settings are not compatible with 2d simulation");
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"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(FLERR,
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"Lattice settings are not compatible with 2d simulation");
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"Lattice settings are not compatible with 2d simulation");
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}
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if (spaceflag) {
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@ -293,10 +293,10 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
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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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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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xlattice,ylattice,zlattice);
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}
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}
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@ -308,23 +308,23 @@ Lattice::~Lattice()
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}
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/* ----------------------------------------------------------------------
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check if 3 orientation vectors are mutually orthogonal
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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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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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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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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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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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@ -381,29 +381,29 @@ void Lattice::setup_transform()
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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)
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if (determinant == 0.0)
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error->all(FLERR,"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][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][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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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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@ -420,11 +420,11 @@ void Lattice::setup_transform()
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orienty[2]*orienty[2];
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length = sqrt((double) lensq);
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if (length == 0.0) error->all(FLERR,"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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lensq = orientz[0]*orientz[0] + orientz[1]*orientz[1] +
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orientz[2]*orientz[2];
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length = sqrt((double) lensq);
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@ -549,12 +549,12 @@ void Lattice::cross(double *x, double *y, double *z)
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/* ----------------------------------------------------------------------
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convert x,y,z from lattice coords to box coords (flag = 0) or vice versa
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use new point to expand bounding box (min to max)
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use new point to expand bounding box (min to max)
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------------------------------------------------------------------------- */
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void Lattice::bbox(int flag, double x, double y, double z,
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double &xmin, double &ymin, double &zmin,
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double &xmax, double &ymax, double &zmax)
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double &xmin, double &ymin, double &zmin,
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double &xmax, double &ymax, double &zmax)
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{
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if (flag == 0) lattice2box(x,y,z);
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else box2lattice(x,y,z);
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