Commit 8a507251 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11388 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 677b1142

src/KSPACE/pppm_disp.cpp

+6 −6
Original line number Diff line number Diff line
@@ -274,7 +274,7 @@ void PPPMDisp::init() 
	  else if (mixflag == 2) { k = 3; break; }

	default:

	  sprintf(str, "Unsupported order in kspace_style "

                  "pppm/disp pair_style %s", force->pair_style);

                  "pppm/disp, pair_style %s", force->pair_style);

	  error->all(FLERR,str);

      }

      function[k] = 1;
@@ -381,7 +381,7 @@ void PPPMDisp::init() 
                         "b/c stencil extends beyond neighbor processor");

      iteration++;



      // set grid for dispersion interaction and coulomb interactions!

      // set grid for dispersion interaction and coulomb interactions

 

      set_grid();
@@ -1292,7 +1292,7 @@ void PPPMDisp::init_coeffs() // local pair coeffs 
    err =  bmax/amax;

    if (err > 1.0e-4) {

      char str[128];

      sprintf(str, "Error in splitting of dispersion coeffs is estimated %g %.",err);

      sprintf(str,"Error in splitting of dispersion coeffs is estimated %g%",err);

      error->warning(FLERR, str);

    }

    // set B
@@ -1337,7 +1337,7 @@ void PPPMDisp::init_coeffs() // local pair coeffs 
        if (screen) fprintf(screen,"  Using %d structure factors\n",nsplit);

        if (logfile) fprintf(logfile,"  Using %d structure factors\n",nsplit);

      }

      if (nsplit > 9) error->warning(FLERR, "Simulations might be very slow because of large number of structure factors!");

      if (nsplit > 9) error->warning(FLERR, "Simulations might be very slow because of large number of structure factors");

    }



    memory->destroy(A);
@@ -1354,7 +1354,7 @@ void PPPMDisp::init_coeffs() // local pair coeffs 
    //cannot use sigma, because this has not been set yet

    double **sigma = (double **) force->pair->extract("sigma",tmp);  

    if (!(epsilon&&sigma))

      error->all(FLERR,"epsilon or sigma reference not set by pair style in PPPMDisp");

      error->all(FLERR,"Epsilon or sigma reference not set by pair style in PPPMDisp");

    double eps_i, sigma_i, sigma_n, *bi = B = new double[7*n+7];

    double c[7] = {

      1.0, sqrt(6.0), sqrt(15.0), sqrt(20.0), sqrt(15.0), sqrt(6.0), 1.0};
@@ -2603,7 +2603,7 @@ void PPPMDisp::set_grid() 


      // break loop if the accuracy has been reached or too many loops have been performed

      if (dfkspace <= accuracy) break;

      if (count > 500) error->all(FLERR, "Could not compute grid size for Coulomb interaction!");

      if (count > 500) error->all(FLERR, "Could not compute grid size for Coulomb interaction");

      h *= 0.95;

      h_x = h_y = h_z = h;

    }

src/KSPACE/pppm_disp.h

+46 −160
Original line number Diff line number Diff line
@@ -383,32 +383,36 @@ command-line option when running LAMMPS to see the offending line. 


E: Cannot use PPPMDisp with 2d simulation



UNDOCUMENTED

The kspace style pppm/disp cannot be used in 2d simulations.  You can

use 2d pppm/disp in a 3d simulation; see the kspace_modify command.



E: Cannot use nonperiodic boundaries with PPPMDisp



UNDOCUMENTED

For kspace style pppm/disp, all 3 dimensions must have periodic

boundaries unless you use the kspace_modify command to define a 2d

slab with a non-periodic z dimension.



E: Incorrect boundaries with slab PPPMDisp



UNDOCUMENTED

Must have periodic x,y dimensions and non-periodic z dimension to use

2d slab option with pppm/disp.



E: PPPMDisp coulomb order cannot be greater than %d



UNDOCUMENTED

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 or dispersion component be used.



E: Unsupported order in kspace_style pppm/disp pair_style %s

E: Unsupported order in kspace_style pppm/disp, pair_style %s



UNDOCUMENTED

Only pair styles with 1/r and 1/r^6 dependence are currently supported.



W: Charges are set, but coulombic solver is not used



UNDOCUMENTED

Self-explanatory.



E: Kspace style with selected options requires atom attribute q
@@ -432,35 +436,43 @@ are defined. 


E: Bad TIP4P angle type for PPPMDisp/TIP4P



UNDOCUMENTED

Specified angle type is not valid.



E: Bad TIP4P bond type for PPPMDisp/TIP4P



UNDOCUMENTED

Specified bond type is not valid.



W: Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor



UNDOCUMENTED

This may lead to a larger grid than desired.  See the kspace_modify overlap

command to prevent changing of the PPPM order.



E: PPPMDisp Coulomb grid is too large



UNDOCUMENTED

The global PPPM grid is larger than OFFSET in one or more dimensions.

OFFSET is currently set to 4096.  You likely need to decrease the

requested accuracy.



E: Coulomb PPPMDisp order has been reduced below minorder



UNDOCUMENTED

The default minimum order is 2.  This can be reset by the

kspace_modify minorder command.



W: Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor



UNDOCUMENTED

This may lead to a larger grid than desired.  See the kspace_modify overlap

command to prevent changing of the PPPM order.



E: PPPMDisp Dispersion grid is too large



UNDOCUMENTED

The global PPPM grid is larger than OFFSET in one or more dimensions.

OFFSET is currently set to 4096.  You likely need to decrease the

requested accuracy.



E: Dispersion PPPMDisp order has been reduced below minorder



UNDOCUMENTED

The default minimum order is 2.  This can be reset by the

kspace_modify minorder command.



E: PPPM grid stencil extends beyond nearest neighbor processor
@@ -468,28 +480,30 @@ This is not allowed if the kspace_modify overlap setting is no. 


E: Matrix factorization to split dispersion coefficients failed



UNDOCUMENTED

This should not normally happen.  Contact the developers.



W: Error in splitting of dispersion coeffs is estimated %g %.

W: Error in splitting of dispersion coeffs is estimated %g%



UNDOCUMENTED

Error is greater than 0.0001 percent.



W: Simulations might be very slow because of large number of structure factors!

W: Simulations might be very slow because of large number of structure factors



UNDOCUMENTED

Self-explanatory.



E: epsilon or sigma reference not set by pair style in PPPMDisp

E: Epsilon or sigma reference not set by pair style in PPPMDisp



UNDOCUMENTED

Self-explanatory.



E: KSpace accuracy too large to estimate G vector



Reduce the accuracy request or specify gwald explicitly

via the kspace_modify command.



E: Could not compute grid size for Coulomb interaction!

E: Could not compute grid size for Coulomb interaction



UNDOCUMENTED

The code is unable to compute a grid size consistent with the desired

accuracy.  This error should not occur for typical problems.  Please

send an email to the developers.



E: Could not compute g_ewald
@@ -499,7 +513,9 @@ send an email to the developers. 


E: Could not adjust g_ewald_6



UNDOCUMENTED

The Newton-Raphson solver failed to converge to a good value for

g_ewald.  This error should not occur for typical problems.  Please

send an email to the developers.



E: Cannot compute initial g_ewald_disp
@@ -507,145 +523,15 @@ LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6 
factor that partitions the computation between real space and k-space

for Disptersion interactions.



E: Could not compute grid size for Dispersion!

E: Could not compute grid size for Dispersion



UNDOCUMENTED

The code is unable to compute a grid size consistent with the desired

accuracy.  This error should not occur for typical problems.  Please

send an email to the developers.



E: Out of range atoms - cannot compute PPPMDisp



UNDOCUMENTED















U: Unsupported mixing rule in kspace_style pppm/disp for pair_style %s



UNDOCUMENTED



U: Cannot (yet) use PPPMDisp with triclinic box



UNDOCUMENTED



U: Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor.



UNDOCUMENTED



U: Reducing PPPMDisp dispersion order b/c stencil extends beyond

neighbor processor



UNDOCUMENTED



U: PPPMDisp dispersion grid is too large



UNDOCUMENTED



U: Could not compute grid size for dispersion



UNDOCUMENTED



U: Cannot (yet) use PPPM_disp with triclinic box



This feature is not yet supported.



U: Cannot use PPPM_disp with 2d simulation



The kspace style pppm_disp cannot be used in 2d simulations.  You can use

2d PPPM_disp in a 3d simulation; see the kspace_modify command.



U: Cannot use nonperiodic boundaries with PPPM_disp



For kspace style pppm_disp, all 3 dimensions must have periodic boundaries

unless you use the kspace_modify command to define a 2d slab with a

non-periodic z dimension.



U: Incorrect boundaries with slab PPPM_disp



Must have periodic x,y dimensions and non-periodic z dimension to use

2d slab option with PPPM_disp.



U: PPPM_disp coulomb order cannot be greater than %d



Self-explanatory.



U: PPPM_disp dispersion order cannot be greater than %d



Self-explanatory.



U: Unsupported mixing rule in kspace_style pppm_disp for pair_style %s



PPPM_disp requires arithemtic or geometric mixing rules.



U: Unsupported order in kspace_style pppm_disp pair_style %s



PPPM_disp only works for 1/r and 1/r^6 potentials



U: Charges are set, but coulombic long-range solver is not used.



Charges have been specified, however, calculations are performed

as if they were zero.



U: Bad TIP4P angle type for PPPM_disp/TIP4P



Specified angle type is not valid.



U: Bad TIP4P bond type for PPPM_disp/TIP4P



Specified bond type is not valid.



U: Reducing PPPM_disp Coulomb order b/c stencil extends beyond neighbor processor



LAMMPS is attempting this in order to allow the simulation

to run.  It should not effect the PPPM_disp accuracy.



U: Reducing PPPM_disp dispersion order b/c stencil extends beyond neighbor processor



LAMMPS is attempting this in order to allow the simulation

to run.  It should not effect the PPPM_disp accuracy.



U: PPPM_disp Coulomb grid is too large



The global PPPM_disp grid for Coulomb interactions is larger than

OFFSET in one or more dimensions.  OFFSET is currently set to 16384.

You likely need to decrease the requested precision.



U: PPPM_grid dispersion grid is too large



One of the PPPM_disp grids for dispersion interactions is larger than

OFFSET in one or more dimensions.  OFFSET is currently set to 16384.

You likely need to decrease the requested precision.



U: Coulomb PPPM_disp order has been reduced to 0



LAMMPS has attempted to reduce the PPPM_disp coulomb order to enable

the simulation to run, but can reduce the order no further.  Try

increasing the accuracy of PPPM_disp coulomb by reducing the tolerance

size, thus inducing a larger PPPM_disp coulomb grid.



U: Dispersion PPPM_disp order has been reduced to 0



LAMMPS has attempted to reduce the PPPM_disp dispersion order to

enable the simulation to run, but can reduce the order no further.

Try increasing the accuracy of PPPM_disp dispersion by reducing the

tolerance size, thus inducing a larger PPPM_disp dispersion grid.



U: Cannot compute PPPM_disp g_ewald



LAMMPS failed to compute a valid approximation for the PPPM_disp

g_ewald factor that partitions the computation between real space and

k-space for Coulomb interactions.



U: Cannot compute final g_ewald_disp



LAMMPS failed to compute a final value for the PPPM_disp g_ewald_6

factor that partitions the computation between real space and k-space

for Disptersion interactions.



U: Out of range atoms - cannot compute PPPM_disp



One or more atoms are attempting to map their charge to a PPPM_disp grid

One or more atoms are attempting to map their charge to a PPPM grid

point that is not owned by a processor.  This is likely for one of two

reasons, both of them bad.  First, it may mean that an atom near the

boundary of a processor's sub-domain has moved more than 1/2 the

src/molecule.h

+45 −38
Original line number Diff line number Diff line
@@ -150,154 +150,161 @@ class Molecule : protected Pointers { 


E: Molecule template ID must be alphanumeric or underscore characters



UNDOCUMENTED

Self-explanatory.



E: Insufficient Jacobi rotations for rigid molecule



UNDOCUMENTED

Eigensolve for rigid body was not sufficiently accurate.



E: Unexpected end of molecule file



UNDOCUMENTED

Self-explanatory.



E: Molecule file z center-of-mass must be 0.0 for 2d



UNDOCUMENTED

Self-explanatory.



E: No atom count in molecule file



UNDOCUMENTED

Self-explanatory.



E: Molecule file has bonds but no nbonds setting



UNDOCUMENTED

Self-explanatory.



E: Molecule file has angles but no nangles setting



UNDOCUMENTED

Self-explanatory.



E: Molecule file has dihedrals but no ndihedrals setting



UNDOCUMENTED

Self-explanatory.



E: Molecule file has impropers but no nimpropers setting



UNDOCUMENTED

Self-explanatory.



E: Molecule file shake flags not before shake atoms



UNDOCUMENTED

The order of the two sections is important.



E: Molecule file shake flags not before shake bonds



UNDOCUMENTED

The order of the two sections is important.



E: Unknown section in molecule file



UNDOCUMENTED

Self-explanatory.



E: Molecule file needs both Special Bond sections



UNDOCUMENTED

Self-explanatory.



E: Molecule file has special flags but no bonds



UNDOCUMENTED

Self-explanatory.



E: Molecule file shake info is incomplete



UNDOCUMENTED

All 3 SHAKE sections are needed.



E: Molecule file z coord must be 0.0 for 2d



UNDOCUMENTED

Self-explanatory.



E: Invalid atom type in molecule file



UNDOCUMENTED

Atom types must range from 1 to specified # of types.



E: Invalid atom diameter in molecule file



UNDOCUMENTED

Diameters must be >= 0.0.



E: Invalid atom mass in molecule file



UNDOCUMENTED

Masses must be > 0.0.



E: Invalid atom ID in Bonds section of molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid bond type in Bonds section of molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid atom ID in Angles section of molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid angle type in Angles section of molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid atom ID in dihedrals section of molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid dihedral type in dihedrals section of molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid atom ID in impropers section of molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid improper type in impropers section of molecule file



UNDOCUMENTED

Self-explanatory.



E: Molecule file special list does not match special count



UNDOCUMENTED

The number of values in an atom's special list does not match count.



E: Invalid special atom index in molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid shake flag in molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid shake atom in molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid shake bond type in molecule file



UNDOCUMENTED

Self-explanatory.



E: Invalid shake angle type in molecule file



UNDOCUMENTED

Self-explanatory.



W: Molecule attributes do not match system attributes



UNDOCUMENTED

An attribute is specified (e.g. diameter, charge) that is

not defined for the specified atom style.



E: Molecule topology type exceeds system topology type



UNDOCUMENTED

The number of bond, angle, etc types in the molecule exceeds the

system setting.  See the create_box command for how to specify these

values.



E: Molecule toplogy/atom exceeds system topology/atom



UNDOCUMENTED

The number of bonds, angles, etc per-atom in the molecule exceeds the

system setting.  See the create_box command for how to specify these

values.



W: Molecule has bond topology but no special bond settings



UNDOCUMENTED

This means the bonded atoms will not be excluded in pair-wise

interactions.



E: Cannot open molecule file %s



UNDOCUMENTED

The specified file cannot be opened.  Check that the path and name are

correct.



*/

src/read_restart.h

+22 −14
Original line number Diff line number Diff line
@@ -97,7 +97,7 @@ Self-explanatory. 


E: Invalid flag in peratom section of restart file



UNDOCUMENTED

The format of this section of the file is not correct.



E: Did not assign all atoms correctly
@@ -116,7 +116,10 @@ When using a "*" in the restart file name, no matching file was found. 


E: Restart file incompatible with current version



UNDOCUMENTED

This is probably because you are trying to read a file created with a

version of LAMMPS that is too old compared to the current version.

Use your older version of LAMMPS and convert the restart file

to a data file.



E: Smallint setting in lmptype.h is not compatible
@@ -125,17 +128,18 @@ you are running. 


E: Imageint setting in lmptype.h is not compatible



UNDOCUMENTED

Format of imageint stored in restart file is not consistent with

LAMMPS version you are running.  See the settings in src/lmptype.h



E: Tagint setting in lmptype.h is not compatible



Smallint stored in restart file is not consistent with LAMMPS version

you are running.

Format of tagint stored in restart file is not consistent with LAMMPS

version you are running.  See the settings in src/lmptype.h



E: Bigint setting in lmptype.h is not compatible



Bigint stored in restart file is not consistent with LAMMPS version

you are running.

Format of bigint stored in restart file is not consistent with LAMMPS

version you are running.  See the settings in src/lmptype.h



E: Cannot run 2d simulation with nonperiodic Z dimension
@@ -182,30 +186,34 @@ Unrecognized entry in restart file. 


E: Restart file is not a multi-proc file



UNDOCUMENTED

The file is inconsistent with the filename you specified for it.



E: Restart file is a multi-proc file



UNDOCUMENTED

The file is inconsistent with the filename you specified for it.



E: Restart file is a MPI-IO file



UNDOCUMENTED

The file is inconsistent with the filename you specified for it.



E: Restart file is not a MPI-IO file



UNDOCUMENTED

The file is inconsistent with the filename you specified for it.



E: Invalid LAMMPS restart file



UNDOCUMENTED

The file does not appear to be a LAMMPS restart file since

it doesn't contain the correct magic string at the beginning.



E: Restart file byte ordering is swapped



UNDOCUMENTED

The file was written on a machine with different byte-ordering than

the machine you are reading it on.  Convert it to a text data file

instead, on the machine you wrote it on.



E: Restart file byte ordering is not recognized



UNDOCUMENTED

The file does not appear to be a LAMMPS restart file since it doesn't

contain a recognized byte-orderomg flag at the beginning.



*/

src/set.h

+8 −7
Original line number Diff line number Diff line
@@ -88,11 +88,11 @@ Self-explanatory. 


E: Invalid density in set command



UNDOCUMENTED

Density must be > 0.0.



E: Invalid volume in set command



UNDOCUMENTED

Volume must be > 0.0.



E: Cannot set non-zero image flag for non-periodic dimension
@@ -104,11 +104,11 @@ Self-explanatory. 


E: Set command integer vector does not exist



UNDOCUMENTED

Self-explanatory.



E: Set command floating point vector does not exist



UNDOCUMENTED

Self-explanatory.



E: Cannot use set atom with no atom IDs defined
@@ -152,7 +152,8 @@ Self-explanatory. 


E: Cannot set bond topology types for atom style template



UNDOCUMENTED

The bond, angle, etc types cannot be changed for this atom style since

they are static settings in the molecule template files.



E: Bond atom missing in set command
@@ -180,10 +181,10 @@ atoms are too far apart to make a valid improper. 


E: Variable name for set command does not exist



UNDOCUMENTED

Self-explanatory.



E: Variable for set command is invalid style



UNDOCUMENTED

Only atom-style variables can be used.



*/

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