ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9567 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2013-03-05 00:00:50 +00:00
parent a5c6bfb1c5
commit a746d1ce48
33 changed files with 86 additions and 148 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
src/BODY/body_nparticle.cpp
View File

@ -97,10 +97,10 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
// error in data file if any values are NULL
for (int i = 0; i < ninteger; i++)
if (ifile[0] == NULL)
if (ifile[i] == NULL)
error->one(FLERR,"Invalid format in Bodies section of data file");
for (int i = 0; i < ndouble; i++)
if (dfile[0] == NULL)
if (dfile[i] == NULL)
error->one(FLERR,"Invalid format in Bodies section of data file");
// set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles

17
src/BODY/body_nparticle.h
View File

@ -52,6 +52,23 @@ E: Invalid body nparticle command
Arguments in atom-style command are not correct.
E: Invalid format in Bodies section of data file
The specified number of integer or floating point values does not
appear.
E: Incorrect # of integer values in Bodies section of data file
See doc page for body style.
E: Incorrect integer value in Bodies section of data file
See doc page for body style.
E: Incorrect # of floating-point values in Bodies section of data file
See doc page for body style.
E: Insufficient Jacobi rotations for body nparticle
Eigensolve for rigid body was not sufficiently accurate.

2
src/CLASS2/pair_lj_class2_coul_long.h
View File

@ -74,6 +74,6 @@ The atom style defined does not have this attribute.
E: Pair style requires a KSpace style
This pair style is designed for use with a KSpace style.
No kspace style is defined.
*/

2
src/COLLOID/pair_colloid.h
View File

@ -60,7 +60,7 @@ class PairColloid : public Pair {
E: Overlapping small/large in pair colloid
This potential is inifinte when there is an overlap.
This potential is infinite when there is an overlap.
E: Overlapping large/large in pair colloid

2
src/GPU/pppm_gpu.cpp
View File

@ -137,7 +137,7 @@ void PPPMGPU::init()
// unsupported option
if (differentiation_flag == 1)
error->all(FLERR,"Cannot do analytic differentiation with pppm/gpu");
error->all(FLERR,"Cannot (yet) do analytic differentiation with pppm/gpu");
if (strcmp(update->integrate_style,"verlet/split") == 0) {
kspace_split=true;

4
src/KSPACE/ewald.h
View File

@ -108,7 +108,7 @@ Must have periodic x,y dimensions and non-periodic z dimension to use
E: KSpace style is incompatible with Pair style
Setting a kspace style requires that a pair style with a long-range
Coulombic component be selected.
Coulombic or dispersion component be used.
E: Cannot use kspace solver on system with no charge
@ -117,7 +117,7 @@ No atoms in system have a non-zero charge.
W: System is not charge neutral, net charge = %g
The total charge on all atoms on the system is not 0.0, which
is not valid for Ewald or PPPM.
is not valid for the long-range Coulombic solvers.
E: KSpace accuracy must be > 0

4
src/KSPACE/ewald_disp.h
View File

@ -120,7 +120,7 @@ Must have periodic x,y dimensions and non-periodic z dimension to use
E: KSpace style is incompatible with Pair style
Setting a kspace style requires that a pair style with a long-range
Coulombic and Dispersion component be selected.
Coulombic or dispersion component be used.
E: Unsupported mixing rule in kspace_style ewald/disp
@ -138,7 +138,7 @@ charges or change options of the kspace solver/pair style.
W: System is not charge neutral, net charge = %g
The total charge on all atoms on the system is not 0.0, which
is not valid for Ewald or PPPM.
is not valid for the long-range Coulombic solvers.
E: KSpace accuracy too large to estimate G vector

7
src/KSPACE/msm.h
View File

@ -169,8 +169,7 @@ Single precision cannot be used with MSM.
E: KSpace style is incompatible with Pair style
Setting a kspace style requires that a pair style with a long-range
Coulombic component be selected that is compatible with MSM. Note
that TIP4P is not (yet) supported by MSM.
Coulombic or dispersion component be used.
E: Cannot use kspace solver on system with no charge
@ -179,7 +178,7 @@ No atoms in system have a non-zero charge.
E: System is not charge neutral, net charge = %g
The total charge on all atoms on the system is not 0.0, which
is not valid for MSM.
is not valid for the long-range Coulombic solvers.
E: KSpace accuracy must be > 0
@ -195,7 +194,7 @@ E: Too many MSM grid levels
The max number of MSM grid levels is hardwired to 10.
W: MSM mesh too small, increasing to 2 points in each direction)
W: MSM mesh too small, increasing to 2 points in each direction
Self-explanatory.

2
src/KSPACE/pair_born_coul_long.h
View File

@ -80,6 +80,6 @@ An atom style that defines this attribute must be used.
E: Pair style requires a KSpace style
This pair style is designed for use with a KSpace style.
No kspace style is defined.
*/

2
src/KSPACE/pair_buck_coul_long.cpp
View File

@ -353,7 +353,7 @@ void PairBuckCoulLong::init_style()
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all(FLERR,"Pair style requres a KSpace style");
error->all(FLERR,"Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
neighbor->request(this);

4
src/KSPACE/pair_buck_coul_long.h
View File

@ -79,8 +79,8 @@ E: Pair style buck/coul/long requires atom attribute q
The atom style defined does not have these attributes.
E: Pair style requres a KSpace style
E: Pair style requires a KSpace style
This pair style is designed for use with a KSpace style.
No kspace style is defined.
*/

4
src/KSPACE/pair_buck_long_coul_long.h
View File

@ -93,7 +93,7 @@ E: LJ6 off not supported in pair_style buck/long/coul/long
Self-exlanatory.
E: Coulomb cut not supported in pair_style buck/long/coul/long
E: Coulomb cut not supported in pair_style buck/long/coul/coul
Must use long-range Coulombic interactions.
@ -111,7 +111,7 @@ The atom style defined does not have this attribute.
E: Pair style requires a KSpace style
This pair style is designed for use with a KSpace style.
No kspace style is defined.
E: All pair coeffs are not set

2
src/KSPACE/pair_coul_long.h
View File

@ -72,6 +72,6 @@ The atom style defined does not have this attribute.
E: Pair style requires a KSpace style
This pair style is designed for use with a KSpace style.
No kspace style is defined.
*/

2
src/KSPACE/pair_lj_charmm_coul_long.h
View File

@ -99,6 +99,6 @@ rRESPA cutoffs.
E: Pair style requires a KSpace style
This pair style is designed for use with a KSpace style.
No kspace style is defined.
*/

2
src/KSPACE/pair_lj_cut_coul_long.h
View File

@ -82,7 +82,7 @@ The atom style defined does not have this attribute.
E: Pair style requires a KSpace style
This pair style is designed for use with a KSpace style.
No kspace style is defined.
E: Pair cutoff < Respa interior cutoff

2
src/KSPACE/pair_lj_cut_tip4p_long.h
View File

@ -93,7 +93,7 @@ TIP4P potentials assume bond lengths in water are constrained
by a fix shake command.
E: Must use an angle style with TIP4P potential
d
TIP4P potentials assume angles in water are constrained by a fix shake
command.

6
src/KSPACE/pair_lj_long_coul_long.cpp
View File

@ -84,11 +84,13 @@ void PairLJLongCoulLong::settings(int narg, char **arg)
if (!comm->me && ewald_order & (1<<6))
error->warning(FLERR,"Mixing forced for LJ coefficients");
if (!comm->me && ewald_order == ((1<<1) | (1<<6)))
error->warning(FLERR,"Using largest cutoff for pair_style lj/long/coullong");
error->warning(FLERR,
"Using largest cutoff for pair_style lj/long/coul/long");
if (!*(++arg))
error->all(FLERR,"Cutoffs missing in pair_style lj/long/coul/long");
if (!((ewald_order^ewald_off) & (1<<1)))
error->all(FLERR,"Coulomb cut not supported in pair_style lj/long/coul/long");
error->all(FLERR,
"Coulomb cut not supported in pair_style lj/long/coul/long");
cut_lj_global = force->numeric(*(arg++));
if (*arg && ((ewald_order & 0x42) == 0x42))
error->all(FLERR,"Only one cutoff allowed when requesting all long");

2
src/KSPACE/pair_lj_long_coul_long.h
View File

@ -107,7 +107,7 @@ The atom style defined does not have this attribute.
E: Pair style requires a KSpace style
This pair style is designed for use with a KSpace style.
No kspace style is defined.
E: Pair cutoff < Respa interior cutoff

6
src/KSPACE/pair_lj_long_tip4p_long.cpp
View File

@ -452,9 +452,11 @@ void PairLJLongTIP4PLong::settings(int narg, char **arg)
if (!comm->me && ewald_order&(1<<6))
error->warning(FLERR,"Mixing forced for lj coefficients");
if (!comm->me && ewald_order==((1<<1)|(1<<6)))
error->warning(FLERR,"Using largest cutoff for pair_style lj/long/tip4p/long");
error->warning(FLERR,
"Using largest cutoff for pair_style lj/long/tip4p/long");
if (!((ewald_order^ewald_off)&(1<<1)))
error->all(FLERR,"Coulombic cut not supported in pair_style lj/long/tip4p/long");
error->all(FLERR,
"Coulomb cut not supported in pair_style lj/long/tip4p/long");
typeO = force->inumeric(arg[1]);
typeH = force->inumeric(arg[2]);
typeB = force->inumeric(arg[3]);

4
src/KSPACE/pppm.h
View File

@ -232,7 +232,7 @@ This is a limitation of the PPPM implementation in LAMMPS.
E: KSpace style is incompatible with Pair style
Setting a kspace style requires that a pair style with a long-range
Coulombic component be selected.
Coulombic or dispersion component be used.
E: Bond and angle potentials must be defined for TIP4P
@ -254,7 +254,7 @@ No atoms in system have a non-zero charge.
W: System is not charge neutral, net charge = %g
The total charge on all atoms on the system is not 0.0, which
is not valid for Ewald or PPPM.
is not valid for the long-range Coulombic solvers.
W: Reducing PPPM order b/c stencil extends beyond nearest neighbor processor

10
src/KSPACE/pppm_disp.cpp
View File

@ -3009,9 +3009,12 @@ void PPPMDisp::set_n_pppm_6()
count++;
// break loop if the accuracy has been reached or too many loops have been performed
// break loop if the accuracy has been reached
// or too many loops have been performed
if (df_kspace <= accuracy) break;
if (count > 500) error->all(FLERR, "Could not compute grid size for Dispersion!");
if (count > 500)
error->all(FLERR,"Could not compute grid size for dispersion");
h *= 0.95;
h_x = h_y = h_z = h;
}
@ -3033,7 +3036,8 @@ double PPPMDisp::lj_rspace_error()
double rgs = (cutoff_lj*g_ewald_6);
rgs *= rgs;
double rgs_inv = 1.0/rgs;
deltaf = csum/sqrt(natoms*xprd*yprd*zprd_slab*cutoff_lj)*sqrt(MY_PI)*pow(g_ewald_6, 5)*
deltaf = csum/sqrt(natoms*xprd*yprd*zprd_slab*cutoff_lj)*
sqrt(MY_PI)*pow(g_ewald_6,5)*
exp(-rgs)*(1+rgs_inv*(3+rgs_inv*(6+rgs_inv*6)));
return deltaf;
}

4
src/KSPACE/pppm_disp.h
View File

@ -383,7 +383,7 @@ This is a limitation of the PPPM implementation in LAMMPS.
E: KSpace style is incompatible with Pair style
Setting a kspace style requires that a pair style with a long-range
Coulombic and Dispersion component be selected.
Coulombic or dispersion component be used.
E: Unsupported mixing rule in kspace_style pppm/disp for pair_style %s
@ -411,7 +411,7 @@ options of the kspace solver/pair style.
W: System is not charge neutral, net charge = %g
The total charge on all atoms on the system is not 0.0, which
is not valid for Ewald or PPPM coulombic solvers.
is not valid for the long-range Coulombic solvers.
E: Bond and angle potentials must be defined for TIP4P

80
src/KSPACE/pppm_old.h
View File

@ -167,84 +167,4 @@ class PPPMOld : public KSpace {
/* ERROR/WARNING messages:
E: Illegal ... command
UNDOCUMENTED
E: Cannot (yet) use PPPM with triclinic box
UNDOCUMENTED
E: Cannot use PPPM with 2d simulation
UNDOCUMENTED
E: Kspace style requires atom attribute q
UNDOCUMENTED
E: Cannot use nonperiodic boundaries with PPPM
UNDOCUMENTED
E: Incorrect boundaries with slab PPPM
UNDOCUMENTED
E: PPPM order cannot be < 2 or > than %d
UNDOCUMENTED
E: KSpace style is incompatible with Pair style
UNDOCUMENTED
E: Bond and angle potentials must be defined for TIP4P
UNDOCUMENTED
E: Bad TIP4P angle type for PPPM/TIP4P
UNDOCUMENTED
E: Bad TIP4P bond type for PPPM/TIP4P
UNDOCUMENTED
E: Cannot use kspace solver on system with no charge
UNDOCUMENTED
W: System is not charge neutral, net charge = %g
UNDOCUMENTED
W: Reducing PPPM order b/c stencil extends beyond neighbor processor
UNDOCUMENTED
E: PPPM grid is too large
UNDOCUMENTED
E: PPPM order has been reduced to 0
UNDOCUMENTED
E: KSpace accuracy must be > 0
UNDOCUMENTED
E: Cannot compute PPPM G
UNDOCUMENTED
E: Out of range atoms - cannot compute PPPM
UNDOCUMENTED
E: Cannot (yet) use K-space slab correction with compute group/group
UNDOCUMENTED
*/

3
src/MC/fix_gcmc.cpp
View File

@ -100,7 +100,8 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
// error checks on region and its extent being inside simulation box
region_xlo = region_xhi = region_ylo = region_yhi = region_zlo = region_zhi = 0.0;
region_xlo = region_xhi = region_ylo = region_yhi =
region_zlo = region_zhi = 0.0;
if (regionflag) {
if (domain->regions[iregion]->bboxflag == 0)
error->all(FLERR,"Fix gcmc region does not support a bounding box");

8
src/MC/fix_gcmc.h
View File

@ -205,14 +205,6 @@ E: Fix gcmc incorrect number of atoms per molecule
The number of atoms in each gas molecule was not computed correctly.
E: Fix gcmc region cannot be dynamic
Only static regions can be used with fix gcmc.
E: Fix gcmc region extends outside simulation box
Self-explanatory.
E: Region ID for fix gcmc does not exist
Self-explanatory.

8
src/RIGID/fix_rigid_nh.h
View File

@ -133,13 +133,13 @@ E: Fix rigid npt/nph dilate group ID does not exist
Self-explanatory.
E: Temperature ID for fix rigid nvt/npt does not exist
E: Temperature ID for fix rigid nvt/npt/nph does not exist
Self-explanatory
Self-explanatory.
E: fix rigid npt/nph does not yet allow triclinic box
E: Fix rigid npt/nph does not yet allow triclinic box
This is a current restriction of the command.
Self-explanatory.
E: Cannot use fix rigid npt/nph and fix deform on same component of stress tensor

12
src/RIGID/fix_rigid_nvt.h
View File

@ -37,12 +37,6 @@ class FixRigidNVT : public FixRigidNH {
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Did not set temperature for fix rigid/nvt
The temp keyword must be specified.
@ -55,6 +49,12 @@ E: Fix rigid/nvt period must be > 0.0
Self-explanatory.
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Fix rigid/nvt temperature order must be 3 or 5
Self-explanatory.

2
src/SHOCK/fix_append_atoms.cpp
View File

@ -127,7 +127,7 @@ FixAppendAtoms::FixAppendAtoms(LAMMPS *lmp, int narg, char **arg) :
} 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,"Fis append/atoms requires a lattice be defined");
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)

12
src/atom_vec_body.cpp
View File

@ -1422,7 +1422,7 @@ void AtomVecBody::check(int flag)
for (int i = 0; i < atom->nlocal; i++) {
if (atom->body[i] >= 0 && atom->body[i] >= nlocal_bonus) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
error->one(FLERR,"BAD AAA");
errorx->one(FLERR,"BAD AAA");
}
}
for (int i = atom->nlocal; i < atom->nlocal+atom->nghost; i++) {
@ -1430,32 +1430,32 @@ void AtomVecBody::check(int flag)
(atom->body[i] < nlocal_bonus ||
atom->body[i] >= nlocal_bonus+nghost_bonus)) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
error->one(FLERR,"BAD BBB");
errorx->one(FLERR,"BAD BBB");
}
}
for (int i = 0; i < nlocal_bonus; i++) {
if (bonus[i].ilocal < 0 || bonus[i].ilocal >= atom->nlocal) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
error->one(FLERR,"BAD CCC");
errorx->one(FLERR,"BAD CCC");
}
}
for (int i = 0; i < nlocal_bonus; i++) {
if (atom->body[bonus[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
error->one(FLERR,"BAD DDD");
errorx->one(FLERR,"BAD DDD");
}
}
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
if (bonus[i].ilocal < atom->nlocal ||
bonus[i].ilocal >= atom->nlocal+atom->nghost) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
error->one(FLERR,"BAD EEE");
errorx->one(FLERR,"BAD EEE");
}
}
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
if (atom->body[bonus[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
error->one(FLERR,"BAD FFF");
errorx->one(FLERR,"BAD FFF");
}
}
}

4
src/input.h
View File

@ -156,6 +156,10 @@ E: Invalid variable name
Variable name used in an input script line is invalid.
E: Invalid immediate variable
Syntax of immediate value is incorrect.
E: Substitution for illegal variable
Input script line contained a variable that could not be substituted

7
src/kspace.h
View File

@ -162,11 +162,8 @@ No pair style is defined.
E: KSpace style is incompatible with Pair style
The Ewald and PPPM solvers work with pair styles with a "coul/long" in
their name. The MSM solver with pair styles with a "coul/msm" in
their name, The dispersion solvers with pair styles with a "lj/long"
in the name. The TIP4P solvers with pair styles with a "tip4p" in the
name.
Setting a kspace style requires that a pair style with a long-range
Coulombic or dispersion component be used.
W: For better accuracy use 'pair_modify table 0'

2
src/pair.cpp
View File

@ -255,7 +255,7 @@ void Pair::init_tables(double cut_coul, double *cut_respa)
double qqrd2e = force->qqrd2e;
if (force->kspace == NULL)
error->all(FLERR,"Pair style requres a KSpace style");
error->all(FLERR,"Pair style requires a KSpace style");
double g_ewald = force->kspace->g_ewald;
double cut_coulsq = cut_coul * cut_coul;

2
src/pair.h
View File

@ -236,7 +236,7 @@ E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Pair style requres a KSpace style
E: Pair style requires a KSpace style
No kspace style is defined.