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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9913 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-05-24 18:55:24 +00:00
parent 3452583172
commit db8eda0253
26 changed files with 24 additions and 99 deletions
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2
src/GPU/Package.sh
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@ -1,6 +1,6 @@
# Update package files in LAMMPS
# cp package file to src if doesn't exist or is different
# do not copy gayberne files if non-GPU version does not exist
# do not copy dependent files if non-GPU version does not exist
for file in *.cpp *.h; do
if (test $file = pair_gayberne_gpu.cpp -a ! -e ../pair_gayberne.cpp) then

2
src/OPT/Package.sh
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@ -1,6 +1,6 @@
# Update package files in LAMMPS
# cp package file to src if doesn't exist or is different
# do not copy eam and charmm files if non-OPT versions do not exist
# do not copy dependent files if non-OPT versions do not exist
for file in *.cpp *.h; do
if (test $file = pair_eam_opt.cpp -a ! -e ../pair_eam.cpp) then

5
src/PERI/pair_peri_lps.cpp
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@ -421,12 +421,11 @@ void PairPeriLPS::init_style()
{
// error checks
if (!atom->peri_flag) error->all(FLERR,"Pair style peri requires atom style peri");
if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
if (domain->lattice == NULL)
error->all(FLERR,"Pair peri requires a lattice be defined");
if (domain->lattice->xlattice != domain->lattice->ylattice ||
domain->lattice->xlattice != domain->lattice->zlattice ||
domain->lattice->ylattice != domain->lattice->zlattice)

5
src/PERI/pair_peri_pmb.cpp
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@ -359,12 +359,11 @@ void PairPeriPMB::init_style()
{
// error checks
if (!atom->peri_flag) error->all(FLERR,"Pair style peri requires atom style peri");
if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
if (domain->lattice == NULL)
error->all(FLERR,"Pair peri requires a lattice be defined");
if (domain->lattice->xlattice != domain->lattice->ylattice ||
domain->lattice->xlattice != domain->lattice->zlattice ||
domain->lattice->ylattice != domain->lattice->zlattice)

9
src/SHOCK/fix_append_atoms.cpp
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@ -60,7 +60,7 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
randomx = NULL;
randomt = NULL;
if (!domain->lattice)
if (domain->lattice->nbasis == 0)
error->all(FLERR,"Fix append/atoms requires a lattice be defined");
nbasis = domain->lattice->nbasis;
@ -126,12 +126,10 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
iarg += 3;
} else if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix append/atoms command");
if (domain->lattice == NULL)
error->all(FLERR,"Fix append/atoms requires a lattice be defined");
int ibasis = atoi(arg[iarg+1]);
int itype = atoi(arg[iarg+2]);
if (ibasis <= 0 || ibasis > nbasis || itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Illegal fix append/atoms command");
error->all(FLERR,"Invalid basis setting in fix append/atoms command");
basistype[ibasis-1] = itype;
iarg += 3;
} else if (strcmp(arg[iarg],"size") == 0) {
@ -184,9 +182,6 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix append/atoms with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;

3
src/SHOCK/fix_wall_piston.cpp
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@ -140,9 +140,6 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix wall/piston with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;

3
src/SRD/fix_wall_srd.cpp
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@ -127,9 +127,6 @@ FixWallSRD::FixWallSRD(LAMMPS *lmp, int narg, char **arg) :
if (wallstyle[m] == CONSTANT) flag = 1;
if (flag) {
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix wall with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;

1
src/USER-MOLFILE/Package.sh
View File

@ -1,5 +1,6 @@
# Update package files in LAMMPS
# copy package file to src if it doesn't exists or is different
for file in molfile_interface.cpp molfile_interface.h molfile_plugin.h \
dump_molfile.cpp dump_molfile.h reader_molfile.h reader_molfile.cpp \
vmdplugin.h ; do \

3
src/change_box.cpp
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@ -185,9 +185,6 @@ void ChangeBox::command(int narg, char **arg)
for (int i = 0; i < nops; i++)
if (ops[i].style == FINAL || ops[i].style == DELTA) flag = 1;
if (flag && scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of change_box with undefined lattice");
if (flag && scaleflag) {
scale[0] = domain->lattice->xlattice;
scale[1] = domain->lattice->ylattice;

3
src/compute_temp_ramp.cpp
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@ -59,9 +59,6 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of compute temp/ramp with undefined lattice");
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;

20
src/create_atoms.cpp
View File

@ -91,22 +91,18 @@ void CreateAtoms::command(int narg, char **arg)
int scaleflag = 1;
remapflag = 0;
if (domain->lattice) {
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = itype;
}
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = itype;
while (iarg < narg) {
if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
if (domain->lattice == NULL)
error->all(FLERR,"Cannot create atoms with undefined lattice");
int ibasis = atoi(arg[iarg+1]);
itype = atoi(arg[iarg+2]);
if (ibasis <= 0 || ibasis > nbasis ||
itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Illegal create_atoms command");
error->all(FLERR,"Invalid basis setting in create_atoms command");
basistype[ibasis-1] = itype;
iarg += 3;
} else if (strcmp(arg[iarg],"remap") == 0) {
@ -131,18 +127,16 @@ void CreateAtoms::command(int narg, char **arg)
if (seed <= 0) error->all(FLERR,"Illegal create_atoms command");
}
// demand lattice be defined
// else setup scaling for single atom
// demand non-none lattice be defined for BOX and REGION
// else setup scaling for SINGLE and RANDOM
// could use domain->lattice->lattice2box() to do conversion of
// lattice to box, but not consistent with other uses of units=lattice
// triclinic remapping occurs in add_single()
if (style == BOX || style == REGION) {
if (domain->lattice == NULL)
if (nbasis == 0)
error->all(FLERR,"Cannot create atoms with undefined lattice");
} else if (scaleflag == 1) {
if (domain->lattice == NULL)
error->all(FLERR,"Cannot create atoms with undefined lattice");
xone[0] *= domain->lattice->xlattice;
xone[1] *= domain->lattice->ylattice;
xone[2] *= domain->lattice->zlattice;

3
src/displace_atoms.cpp
View File

@ -77,9 +77,6 @@ void DisplaceAtoms::command(int narg, char **arg)
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of displace_atoms with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;

10
src/domain.cpp
View File

@ -85,6 +85,11 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
boxhi_lamda[0] = boxhi_lamda[1] = boxhi_lamda[2] = 1.0;
lattice = NULL;
char **args = new char*[2];
args[0] = (char *) "none";
args[1] = (char *) "1.0";
set_lattice(2,args);
nregion = maxregion = 0;
regions = NULL;
}
@ -1229,17 +1234,12 @@ void Domain::image_flip(int m, int n, int p)
/* ----------------------------------------------------------------------
create a lattice
delete it if style = none
------------------------------------------------------------------------- */
void Domain::set_lattice(int narg, char **arg)
{
if (lattice) delete lattice;
lattice = new Lattice(lmp,narg,arg);
if (lattice->style == 0) {
delete lattice;
lattice = NULL;
}
}
/* ----------------------------------------------------------------------

3
src/fix_ave_spatial.cpp
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@ -340,9 +340,6 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,
"Fix ave/spatial for triclinic boxes requires units reduced");
if (scaleflag == LATTICE && domain->lattice == NULL)
error->all(FLERR,"Use of fix ave/spatial with undefined lattice");
if (scaleflag == LATTICE) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;

3
src/fix_deform.cpp
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@ -256,9 +256,6 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (set[i].style == FINAL || set[i].style == DELTA ||
set[i].style == VEL || set[i].style == WIGGLE) flag = 1;
if (flag && scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix deform with undefined lattice");
double xscale,yscale,zscale;
if (flag && scaleflag) {
xscale = domain->lattice->xlattice;

3
src/fix_deposit.cpp
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@ -98,9 +98,6 @@ FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix deposit with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;

2
src/fix_dt_reset.cpp
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@ -83,8 +83,6 @@ FixDtReset::FixDtReset(LAMMPS *lmp, int narg, char **arg) :
// setup scaling, based on xlattice parameter
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix dt/reset with undefined lattice");
if (scaleflag) xmax *= domain->lattice->xlattice;
// initializations

3
src/fix_indent.cpp
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@ -59,9 +59,6 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) :
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix indent with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;

3
src/fix_move.cpp
View File

@ -192,9 +192,6 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
if ((mstyle == LINEAR || mstyle == WIGGLE || mstyle == ROTATE) &&
scaleflag) {
if (domain->lattice == NULL)
error->all(FLERR,"Use of fix move with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;

3
src/fix_recenter.cpp
View File

@ -75,9 +75,6 @@ FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) :
// scale xcom,ycom,zcom
if (scaleflag == LATTICE && domain->lattice == NULL)
error->all(FLERR,"Use of fix recenter with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag == LATTICE) {
xscale = domain->lattice->xlattice;

3
src/fix_wall.cpp
View File

@ -163,9 +163,6 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
if (xstyle[m] != EDGE) flag = 1;
if (flag) {
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix wall with undefined lattice");
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;

3
src/fix_wall_reflect.cpp
View File

@ -115,9 +115,6 @@ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) :
if (wallstyle[m] != EDGE) flag = 1;
if (flag) {
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of fix wall with undefined lattice");
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;

4
src/lattice.cpp
View File

@ -51,7 +51,9 @@ Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
else error->all(FLERR,"Illegal lattice command");
if (style == NONE) {
if (narg > 1) error->all(FLERR,"Illegal lattice command");
if (narg != 2) error->all(FLERR,"Illegal lattice command");
xlattice = ylattice = zlattice = atof(arg[1]);
if (xlattice <= 0.0) error->all(FLERR,"Illegal lattice command");
return;
}

3
src/region.cpp
View File

@ -368,9 +368,6 @@ void Region::options(int narg, char **arg)
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all(FLERR,"Use of region with undefined lattice");
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;

12
src/thermo.cpp
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@ -741,16 +741,10 @@ void Thermo::parse_fields(char *str)
addfield("Yz",&Thermo::compute_yz,FLOAT);
} else if (strcmp(word,"xlat") == 0) {
if (domain->lattice == NULL)
error->all(FLERR,"Thermo keyword requires lattice be defined");
addfield("Xlat",&Thermo::compute_xlat,FLOAT);
} else if (strcmp(word,"ylat") == 0) {
if (domain->lattice == NULL)
error->all(FLERR,"Thermo keyword requires lattice be defined");
addfield("Ylat",&Thermo::compute_ylat,FLOAT);
} else if (strcmp(word,"zlat") == 0) {
if (domain->lattice == NULL)
error->all(FLERR,"Thermo keyword requires lattice be defined");
addfield("Zlat",&Thermo::compute_zlat,FLOAT);
} else if (strcmp(word,"pxx") == 0) {
@ -1245,16 +1239,10 @@ int Thermo::evaluate_keyword(char *word, double *answer)
else if (strcmp(word,"yz") == 0) compute_yz();
else if (strcmp(word,"xlat") == 0) {
if (domain->lattice == NULL)
error->all(FLERR,"Thermo keyword in variable requires lattice be defined");
compute_xlat();
} else if (strcmp(word,"ylat") == 0) {
if (domain->lattice == NULL)
error->all(FLERR,"Thermo keyword in variable requires lattice be defined");
compute_ylat();
} else if (strcmp(word,"zlat") == 0) {
if (domain->lattice == NULL)
error->all(FLERR,"Thermo keyword in variable requires lattice be defined");
compute_zlat();
} else if (strcmp(word,"pxx") == 0) {

9
src/velocity.cpp
View File

@ -378,20 +378,14 @@ void Velocity::set(int narg, char **arg)
xscale = yscale = zscale = 1.0;
if (xstyle && !xstr) {
if (scale_flag && domain->lattice == NULL)
error->all(FLERR,"Use of velocity with undefined lattice");
if (scale_flag) xscale = domain->lattice->xlattice;
vx *= xscale;
}
if (ystyle && !ystr) {
if (scale_flag && domain->lattice == NULL)
error->all(FLERR,"Use of velocity with undefined lattice");
if (scale_flag) yscale = domain->lattice->ylattice;
vy *= yscale;
}
if (zstyle && !zstr) {
if (scale_flag && domain->lattice == NULL)
error->all(FLERR,"Use of velocity with undefined lattice");
if (scale_flag) zscale = domain->lattice->zlattice;
vz *= zscale;
}
@ -552,9 +546,6 @@ void Velocity::ramp(int narg, char **arg)
{
// set scale factors
if (scale_flag && domain->lattice == NULL)
error->all(FLERR,"Use of velocity with undefined lattice");
if (scale_flag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;