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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7003 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-09-23 18:06:55 +00:00
parent 2d99de131d
commit 19e8c92a90
468 changed files with 4628 additions and 5204 deletions
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70
src/lattice.cpp
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@ -23,8 +23,6 @@
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define BIG 1.0e30
enum{NONE,SC,BCC,FCC,HCP,DIAMOND,SQ,SQ2,HEX,CUSTOM};
@ -38,7 +36,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
// parse style arg
if (narg < 1) error->all("Illegal lattice command");
if (narg < 1) error->all(FLERR,"Illegal lattice command");
if (strcmp(arg[0],"none") == 0) style = NONE;
else if (strcmp(arg[0],"sc") == 0) style = SC;
@ -50,10 +48,10 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
else if (strcmp(arg[0],"sq2") == 0) style = SQ2;
else if (strcmp(arg[0],"hex") == 0) style = HEX;
else if (strcmp(arg[0],"custom") == 0) style = CUSTOM;
else error->all("Illegal lattice command");
else error->all(FLERR,"Illegal lattice command");
if (style == NONE) {
if (narg > 1) error->all("Illegal lattice command");
if (narg > 1) error->all(FLERR,"Illegal lattice command");
return;
}
@ -64,18 +62,18 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (dimension == 2) {
if (style == SC || style == BCC || style == FCC || style == HCP ||
style == DIAMOND)
error->all("Lattice style incompatible with simulation dimension");
error->all(FLERR,"Lattice style incompatible with simulation dimension");
}
if (dimension == 3) {
if (style == SQ || style == SQ2 || style == HEX)
error->all("Lattice style incompatible with simulation dimension");
error->all(FLERR,"Lattice style incompatible with simulation dimension");
}
// scale = conversion factor between lattice and box units
if (narg < 2) error->all("Illegal lattice command");
if (narg < 2) error->all(FLERR,"Illegal lattice command");
scale = atof(arg[1]);
if (scale <= 0.0) error->all("Illegal lattice command");
if (scale <= 0.0) error->all(FLERR,"Illegal lattice command");
// set basis atoms for each style
// x,y,z = fractional coords within unit cell
@ -140,23 +138,23 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
int iarg = 2;
while (iarg < narg) {
if (strcmp(arg[iarg],"origin") == 0) {
if (iarg+4 > narg) error->all("Illegal lattice command");
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
origin[0] = atof(arg[iarg+1]);
origin[1] = atof(arg[iarg+2]);
origin[2] = atof(arg[iarg+3]);
if (origin[0] < 0.0 || origin[0] >= 1.0 ||
origin[1] < 0.0 || origin[1] >= 1.0 ||
origin[2] < 0.0 || origin[2] >= 1.0)
error->all("Illegal lattice command");
error->all(FLERR,"Illegal lattice command");
iarg += 4;
} else if (strcmp(arg[iarg],"orient") == 0) {
if (iarg+5 > narg) error->all("Illegal lattice command");
if (iarg+5 > narg) error->all(FLERR,"Illegal lattice command");
int dim;
if (strcmp(arg[iarg+1],"x") == 0) dim = 0;
else if (strcmp(arg[iarg+1],"y") == 0) dim = 1;
else if (strcmp(arg[iarg+1],"z") == 0) dim = 2;
else error->all("Illegal lattice command");
else error->all(FLERR,"Illegal lattice command");
int *orient;
if (dim == 0) orient = orientx;
else if (dim == 1) orient = orienty;
@ -167,7 +165,7 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
iarg += 5;
} else if (strcmp(arg[iarg],"spacing") == 0) {
if (iarg+4 > narg) error->all("Illegal lattice command");
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
spaceflag = 1;
xlattice = atof(arg[iarg+1]);
ylattice = atof(arg[iarg+2]);
@ -175,67 +173,67 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
iarg += 4;
} else if (strcmp(arg[iarg],"a1") == 0) {
if (iarg+4 > narg) error->all("Illegal lattice command");
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
if (style != CUSTOM)
error->all("Invalid option in lattice command for non-custom style");
error->all(FLERR,"Invalid option in lattice command for non-custom style");
a1[0] = atof(arg[iarg+1]);
a1[1] = atof(arg[iarg+2]);
a1[2] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"a2") == 0) {
if (iarg+4 > narg) error->all("Illegal lattice command");
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
if (style != CUSTOM)
error->all("Invalid option in lattice command for non-custom style");
error->all(FLERR,"Invalid option in lattice command for non-custom style");
a2[0] = atof(arg[iarg+1]);
a2[1] = atof(arg[iarg+2]);
a2[2] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"a3") == 0) {
if (iarg+4 > narg) error->all("Illegal lattice command");
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
if (style != CUSTOM)
error->all("Invalid option in lattice command for non-custom style");
error->all(FLERR,"Invalid option in lattice command for non-custom style");
a3[0] = atof(arg[iarg+1]);
a3[1] = atof(arg[iarg+2]);
a3[2] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+4 > narg) error->all("Illegal lattice command");
if (iarg+4 > narg) error->all(FLERR,"Illegal lattice command");
if (style != CUSTOM)
error->all("Invalid option in lattice command for non-custom style");
error->all(FLERR,"Invalid option in lattice command for non-custom style");
double x = atof(arg[iarg+1]);
double y = atof(arg[iarg+2]);
double z = atof(arg[iarg+3]);
if (x < 0.0 || x >= 1.0 || y < 0.0 || y >= 1.0 || z < 0.0 || z >= 1.0)
error->all("Illegal lattice command");
error->all(FLERR,"Illegal lattice command");
add_basis(x,y,z);
iarg += 4;
} else error->all("Illegal lattice command");
} else error->all(FLERR,"Illegal lattice command");
}
// check settings for errors
if (nbasis == 0) error->all("No basis atoms in lattice");
if (nbasis == 0) error->all(FLERR,"No basis atoms in lattice");
if (!orthogonal())
error->all("Lattice orient vectors are not orthogonal");
error->all(FLERR,"Lattice orient vectors are not orthogonal");
if (!right_handed())
error->all("Lattice orient vectors are not right-handed");
error->all(FLERR,"Lattice orient vectors are not right-handed");
if (collinear())
error->all("Lattice primitive vectors are collinear");
error->all(FLERR,"Lattice primitive vectors are collinear");
if (dimension == 2) {
if (origin[2] != 0.0)
error->all("Lattice settings are not compatible with 2d simulation");
error->all(FLERR,"Lattice settings are not compatible with 2d simulation");
if (orientx[2] != 0 || orienty[2] != 0 ||
orientz[0] != 0 || orientz[1] != 0)
error->all("Lattice settings are not compatible with 2d simulation");
error->all(FLERR,"Lattice settings are not compatible with 2d simulation");
if (a1[2] != 0.0 || a2[2] != 0.0 || a3[0] != 0.0 || a3[1] != 0.0)
error->all("Lattice settings are not compatible with 2d simulation");
error->all(FLERR,"Lattice settings are not compatible with 2d simulation");
}
if (spaceflag) {
if (xlattice <= 0.0 || ylattice <= 0.0 || zlattice <= 0.0)
error->all("Lattice spacings are invalid");
error->all(FLERR,"Lattice spacings are invalid");
}
// reset scale for LJ units (input scale is rho*)
@ -376,7 +374,7 @@ void Lattice::setup_transform()
primitive[0][1]*primitive[1][0]*primitive[2][2] -
primitive[0][2]*primitive[1][1]*primitive[2][0];
if (determinant == 0.0) error->all("Degenerate lattice primitive vectors");
if (determinant == 0.0) error->all(FLERR,"Degenerate lattice primitive vectors");
priminv[0][0] = (primitive[1][1]*primitive[2][2] -
primitive[1][2]*primitive[2][1]) / determinant;
@ -404,7 +402,7 @@ void Lattice::setup_transform()
int lensq = orientx[0]*orientx[0] + orientx[1]*orientx[1] +
orientx[2]*orientx[2];
length = sqrt((double) lensq);
if (length == 0.0) error->all("Zero-length lattice orient vector");
if (length == 0.0) error->all(FLERR,"Zero-length lattice orient vector");
rotaterow[0][0] = orientx[0] / length;
rotaterow[0][1] = orientx[1] / length;
@ -413,7 +411,7 @@ void Lattice::setup_transform()
lensq = orienty[0]*orienty[0] + orienty[1]*orienty[1] +
orienty[2]*orienty[2];
length = sqrt((double) lensq);
if (length == 0.0) error->all("Zero-length lattice orient vector");
if (length == 0.0) error->all(FLERR,"Zero-length lattice orient vector");
rotaterow[1][0] = orienty[0] / length;
rotaterow[1][1] = orienty[1] / length;
@ -422,7 +420,7 @@ void Lattice::setup_transform()
lensq = orientz[0]*orientz[0] + orientz[1]*orientz[1] +
orientz[2]*orientz[2];
length = sqrt((double) lensq);
if (length == 0.0) error->all("Zero-length lattice orient vector");
if (length == 0.0) error->all(FLERR,"Zero-length lattice orient vector");
rotaterow[2][0] = orientz[0] / length;
rotaterow[2][1] = orientz[1] / length;