diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 40f7697847..66bb72846d 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -174,9 +174,10 @@ void FixGPU::init() if (_particle_split < 0) if (force->pair_match("hybrid",1) != NULL || force->pair_match("hybrid/overlay",1) != NULL) - error->all(FLERR,"GPU 'split' must be positive for hybrid pair styles"); + error->all(FLERR,"GPU split param must be positive " + "for hybrid pair styles"); - // Make sure fdotr virial is not accumulated multiple times + // make sure fdotr virial is not accumulated multiple times if (force->pair_match("hybrid",1) != NULL) { PairHybrid *hybrid = (PairHybrid *) force->pair; diff --git a/src/GPU/fix_gpu.h b/src/GPU/fix_gpu.h index 26dc73a5bb..75dd4c8e4f 100644 --- a/src/GPU/fix_gpu.h +++ b/src/GPU/fix_gpu.h @@ -77,31 +77,19 @@ OpenMP support. E: GPU package does not (yet) work with atom_style template -UNDOCUMENTED +Self-explanatory. E: Cannot use pair hybrid with GPU neighbor list builds -UNDOCUMENTED +Neighbor list builds must be done on the CPU for this pair style. -E: GPU 'split' must be positive for hybrid pair styles +E: GPU split param must be positive for hybrid pair styles -UNDOCUMENTED +See the package gpu command. E: Cannot use neigh_modify exclude with GPU neighbor builds This is a current limitation of the GPU implementation in LAMMPS. -U: Cannot use pair hybrid with GPU neighbor builds - -See documentation for fix gpu. - -U: Fix GPU split must be positive for hybrid pair styles - -Self-explanatory. - -U: GPU styles must be on the outmost r-RESPA level - -Self-explanatory. - */ diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 55e5191b0e..5458b5a0a3 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -100,7 +100,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : zlo = ((RegCylinder *) domain->regions[iregion])->lo; zhi = ((RegCylinder *) domain->regions[iregion])->hi; if (axis != 'z') - error->all(FLERR,"Must use a z-axis cylinder with fix pour"); + error->all(FLERR,"Must use a z-axis cylinder region with fix pour"); if (xc-rc < domain->boxlo[0] || xc+rc > domain->boxhi[0] || yc-rc < domain->boxlo[1] || yc+rc > domain->boxhi[1] || zlo < domain->boxlo[2] || zhi > domain->boxhi[2]) diff --git a/src/GRANULAR/fix_pour.h b/src/GRANULAR/fix_pour.h index 39df74b88a..5d7341449d 100644 --- a/src/GRANULAR/fix_pour.h +++ b/src/GRANULAR/fix_pour.h @@ -88,478 +88,146 @@ command-line option when running LAMMPS to see the offending line. E: Fix pour requires atom attributes radius, rmass -UNDOCUMENTED +The atom style defined does not have these attributes. E: Invalid atom type in fix pour command -UNDOCUMENTED +Self-explanatory. E: Must specify a region in fix pour -UNDOCUMENTED +Self-explanatory. E: Fix pour region does not support a bounding box -UNDOCUMENTED +Not all regions represent bounded volumes. You cannot use +such a region with the fix pour command. E: Fix pour region cannot be dynamic -UNDOCUMENTED +Only static regions can be used with fix pour. E: Insertion region extends outside simulation box -UNDOCUMENTED +Self-explanatory. -E: Must use a z-axis cylinder with fix pour - -UNDOCUMENTED - -E: Must use a block or cylinder region with fix pour - -UNDOCUMENTED - -E: Must use a block region with fix pour for 2d simulations - -UNDOCUMENTED - -E: Cannot use fix_pour unless atoms have IDs - -UNDOCUMENTED - -E: Fix pour molecule must have coordinates - -UNDOCUMENTED - -E: Fix pour molecule must have atom types - -UNDOCUMENTED - -E: Invalid atom type in fix pour mol command - -UNDOCUMENTED - -E: Fix pour molecule template ID must be same as atom style template ID - -UNDOCUMENTED - -E: Cannot use fix pour rigid and not molecule - -UNDOCUMENTED - -E: Cannot use fix pour shake and not molecule - -UNDOCUMENTED - -E: Cannot use fix pour rigid and shake - -UNDOCUMENTED - -E: No fix gravity defined for fix pour - -UNDOCUMENTED - -E: Cannot use fix pour with triclinic box - -UNDOCUMENTED - -E: Gravity must point in -z to use with fix pour in 3d - -UNDOCUMENTED - -E: Gravity must point in -y to use with fix pour in 2d - -UNDOCUMENTED - -E: Gravity changed since fix pour was created - -UNDOCUMENTED - -E: Fix pour rigid fix does not exist - -UNDOCUMENTED - -E: Fix pour and fix rigid/small not using same molecule template ID - -UNDOCUMENTED - -E: Fix pour shake fix does not exist - -UNDOCUMENTED - -E: Fix pour and fix shake not using same molecule template ID - -UNDOCUMENTED - -W: Less insertions than requested - -UNDOCUMENTED - -E: Too many total atoms - -UNDOCUMENTED - -E: New atom IDs exceed maximum allowed ID - -UNDOCUMENTED - -E: Fix pour region ID does not exist - -UNDOCUMENTED - -E: Molecule template ID for fix pour does not exist - -UNDOCUMENTED - -W: Molecule template for fix pour has multiple molecules - -UNDOCUMENTED - -E: Fix pour polydisperse fractions do not sum to 1.0 - -UNDOCUMENTED - -E: Cannot change timestep with fix pour - -UNDOCUMENTED - -U: Cannot read_data after simulation box is defined - -The read_data command cannot be used after a read_data, -read_restart, or create_box command. - -U: Cannot run 2d simulation with nonperiodic Z dimension - -Use the boundary command to make the z dimension periodic in order to -run a 2d simulation. - -U: Fix ID for read_data does not exist +E: Must use a z-axis cylinder region with fix pour Self-explanatory. -U: Must read Atoms before Velocities +E: Must use a block or cylinder region with fix pour -The Atoms section of a data file must come before a Velocities -section. +Self-explanatory. -U: Invalid data file section: Bonds +E: Must use a block region with fix pour for 2d simulations -Atom style does not allow bonds. +Self-explanatory. -U: Must read Atoms before Bonds +E: Cannot use fix_pour unless atoms have IDs -The Atoms section of a data file must come before a Bonds section. +Self-explanatory. -U: Invalid data file section: Angles +E: Fix pour molecule must have coordinates -Atom style does not allow angles. +The defined molecule does not specify coordinates. -U: Must read Atoms before Angles +E: Fix pour molecule must have atom types -The Atoms section of a data file must come before an Angles section. +The defined molecule does not specify atom types. -U: Invalid data file section: Dihedrals +E: Invalid atom type in fix pour mol command -Atom style does not allow dihedrals. +The atom types in the defined molecule are added to the value +specified in the create_atoms command, as an offset. The final value +for each atom must be between 1 to N, where N is the number of atom +types. -U: Must read Atoms before Dihedrals +E: Fix pour molecule template ID must be same as atom style template ID -The Atoms section of a data file must come before a Dihedrals section. +When using atom_style template, you cannot pour molecules that are +not in that template. -U: Invalid data file section: Impropers +E: Cannot use fix pour rigid and not molecule -Atom style does not allow impropers. +Self-explanatory. -U: Must read Atoms before Impropers +E: Cannot use fix pour shake and not molecule -The Atoms section of a data file must come before an Impropers -section. +Self-explanatory. -U: Invalid data file section: Ellipsoids +E: Cannot use fix pour rigid and shake -Atom style does not allow ellipsoids. +These two attributes are conflicting. -U: Must read Atoms before Ellipsoids +E: No fix gravity defined for fix pour -The Atoms section of a data file must come before a Ellipsoids -section. +Gravity is required to use fix pour. -U: Invalid data file section: Lines +E: Cannot use fix pour with triclinic box -Atom style does not allow lines. +This option is not yet supported. -U: Must read Atoms before Lines +E: Gravity must point in -z to use with fix pour in 3d -The Atoms section of a data file must come before a Lines section. +Self-explanatory. -U: Invalid data file section: Triangles +E: Gravity must point in -y to use with fix pour in 2d -Atom style does not allow triangles. +Self-explanatory. -U: Must read Atoms before Triangles +E: Gravity changed since fix pour was created -The Atoms section of a data file must come before a Triangles section. +The gravity vector defined by fix gravity must be static. -U: Invalid data file section: Bodies +E: Fix pour rigid fix does not exist -Atom style does not allow bodies. +Self-explanatory. -U: Must read Atoms before Bodies +E: Fix pour and fix rigid/small not using same molecule template ID -The Atoms section of a data file must come before a Bodies section. +Self-explanatory. -U: Must define pair_style before Pair Coeffs +E: Fix pour shake fix does not exist -Must use a pair_style command before reading a data file that defines -Pair Coeffs. +Self-explanatory. -U: Must define pair_style before PairIJ Coeffs +E: Fix pour and fix shake not using same molecule template ID -UNDOCUMENTED +Self-explanatory. -U: Invalid data file section: Bond Coeffs +W: Less insertions than requested -Atom style does not allow bonds. +The fix pour command was unsuccessful at finding open space +for as many particles as it tried to insert. -U: Must define bond_style before Bond Coeffs - -Must use a bond_style command before reading a data file that -defines Bond Coeffs. - -U: Invalid data file section: Angle Coeffs - -Atom style does not allow angles. - -U: Must define angle_style before Angle Coeffs - -Must use an angle_style command before reading a data file that -defines Angle Coeffs. - -U: Invalid data file section: Dihedral Coeffs - -Atom style does not allow dihedrals. - -U: Must define dihedral_style before Dihedral Coeffs - -Must use a dihedral_style command before reading a data file that -defines Dihedral Coeffs. - -U: Invalid data file section: Improper Coeffs - -Atom style does not allow impropers. - -U: Must define improper_style before Improper Coeffs - -Must use an improper_style command before reading a data file that -defines Improper Coeffs. - -U: Invalid data file section: BondBond Coeffs - -Atom style does not allow angles. - -U: Must define angle_style before BondBond Coeffs - -Must use an angle_style command before reading a data file that -defines Angle Coeffs. - -U: Invalid data file section: BondAngle Coeffs - -Atom style does not allow angles. - -U: Must define angle_style before BondAngle Coeffs - -Must use an angle_style command before reading a data file that -defines Angle Coeffs. - -U: Invalid data file section: MiddleBondTorsion Coeffs - -Atom style does not allow dihedrals. - -U: Must define dihedral_style before MiddleBondTorsion Coeffs - -Must use a dihedral_style command before reading a data file that -defines MiddleBondTorsion Coeffs. - -U: Invalid data file section: EndBondTorsion Coeffs - -Atom style does not allow dihedrals. - -U: Must define dihedral_style before EndBondTorsion Coeffs - -Must use a dihedral_style command before reading a data file that -defines EndBondTorsion Coeffs. - -U: Invalid data file section: AngleTorsion Coeffs - -Atom style does not allow dihedrals. - -U: Must define dihedral_style before AngleTorsion Coeffs - -Must use a dihedral_style command before reading a data file that -defines AngleTorsion Coeffs. - -U: Invalid data file section: AngleAngleTorsion Coeffs - -Atom style does not allow dihedrals. - -U: Must define dihedral_style before AngleAngleTorsion Coeffs - -Must use a dihedral_style command before reading a data file that -defines AngleAngleTorsion Coeffs. - -U: Invalid data file section: BondBond13 Coeffs - -Atom style does not allow dihedrals. - -U: Must define dihedral_style before BondBond13 Coeffs - -Must use a dihedral_style command before reading a data file that -defines BondBond13 Coeffs. - -U: Invalid data file section: AngleAngle Coeffs - -Atom style does not allow impropers. - -U: Must define improper_style before AngleAngle Coeffs - -Must use an improper_style command before reading a data file that -defines AngleAngle Coeffs. - -U: Unknown identifier in data file: %s - -A section of the data file cannot be read by LAMMPS. - -U: No atoms in data file - -The header of the data file indicated that atoms would be included, -but they were not present. - -U: Needed molecular topology not in data file - -UNDOCUMENTED - -U: Needed bonus data not in data file - -Some atom styles require bonus data. See the read_data doc page for -details. - -U: Unexpected end of data file - -LAMMPS hit the end of the data file while attempting to read a -section. Something is wrong with the format of the data file. - -U: No ellipsoids allowed with this atom style - -Self-explanatory. Check data file. - -U: No lines allowed with this atom style - -Self-explanatory. Check data file. - -U: No triangles allowed with this atom style - -Self-explanatory. Check data file. - -U: No bodies allowed with this atom style - -Self-explanatory. Check data file. - -U: System in data file is too big +E: Too many total atoms See the setting for bigint in the src/lmptype.h file. -U: No bonds allowed with this atom style +E: New atom IDs exceed maximum allowed ID -Self-explanatory. Check data file. +See the setting for tagint in the src/lmptype.h file. -U: No angles allowed with this atom style +E: Fix pour region ID does not exist -Self-explanatory. Check data file. +Self-explanatory. -U: No dihedrals allowed with this atom style +E: Molecule template ID for fix pour does not exist -Self-explanatory. Check data file. +Self-explanatory. -U: No impropers allowed with this atom style +W: Molecule template for fix pour has multiple molecules -Self-explanatory. Check data file. +The fix pour command will only create molecules of a single type, +i.e. the first molecule in the template. -U: Bonds defined but no bond types +E: Fix pour polydisperse fractions do not sum to 1.0 -The data file header lists bonds but no bond types. +Self-explanatory. -U: Angles defined but no angle types +E: Cannot change timestep with fix pour -The data file header lists angles but no angle types. - -U: Dihedrals defined but no dihedral types - -The data file header lists dihedrals but no dihedral types. - -U: Impropers defined but no improper types - -The data file header lists improper but no improper types. - -U: No molecule topology allowed with atom style template - -UNDOCUMENTED - -U: Did not assign all atoms correctly - -Atoms read in from a data file were not assigned correctly to -processors. This is likely due to some atom coordinates being -outside a non-periodic simulation box. - -U: Bonds assigned incorrectly - -Bonds read in from the data file were not assigned correctly to atoms. -This means there is something invalid about the topology definitions. - -U: Angles assigned incorrectly - -Angles read in from the data file were not assigned correctly to -atoms. This means there is something invalid about the topology -definitions. - -U: Dihedrals assigned incorrectly - -Dihedrals read in from the data file were not assigned correctly to -atoms. This means there is something invalid about the topology -definitions. - -U: Impropers assigned incorrectly - -Impropers read in from the data file were not assigned correctly to -atoms. This means there is something invalid about the topology -definitions. - -U: Too many lines in one body in data file - boost MAXBODY - -MAXBODY is a setting at the top of the src/read_data.cpp file. -Set it larger and re-compile the code. - -U: Cannot open gzipped file - -LAMMPS was compiled without support for reading and writing gzipped -files through a pipeline to the gzip program with -DLAMMPS_GZIP. - -U: Cannot open file %s - -The specified file cannot be opened. Check that the path and name are -correct. If the file is a compressed file, also check that the gzip -executable can be found and run. - -U: Invalid atom ID in Atoms section of data file - -Atom IDs must be positive integers. - -U: Molecular data file has too many atoms - -These kids of data files are currently limited to a number -of atoms that fits in a 32-bit integer. - -U: Needed topology not in data file - -The header of the data file indicated that bonds or angles or -dihedrals or impropers would be included, but they were not present. +This is because fix pour pre-computes the time delay for particles to +fall out of the insertion volume due to gravity. */ diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h index 64cffe4057..65d8573aed 100644 --- a/src/MANYBODY/fix_qeq_comb.h +++ b/src/MANYBODY/fix_qeq_comb.h @@ -77,7 +77,7 @@ An atom style with charge must be used to perform charge equilibration. E: Must use pair_style comb or comb3 with fix qeq/comb -UNDOCUMENTED +Self-explanatory. E: Fix qeq/comb group has no atoms diff --git a/src/MC/fix_bond_break.h b/src/MC/fix_bond_break.h index 6c8f749861..009d516429 100755 --- a/src/MC/fix_bond_break.h +++ b/src/MC/fix_bond_break.h @@ -73,7 +73,8 @@ Self-explanatory. E: Cannot use fix bond/break with non-molecular systems -Self-explanatory. +Only systems with bonds that can be changed can be used. Atom_style +template does not qualify. E: Fix bond/break requires special_bonds = 0,1,1 diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h index 52f9b09de2..0e0e606b9c 100755 --- a/src/MC/fix_bond_create.h +++ b/src/MC/fix_bond_create.h @@ -91,7 +91,8 @@ Self-explanatory. E: Cannot use fix bond/create with non-molecular systems -Self-explanatory. +Only systems with bonds that can be changed can be used. Atom_style +template does not qualify. E: Inconsistent iparam/jparam values in fix bond/create command diff --git a/src/MC/fix_bond_swap.h b/src/MC/fix_bond_swap.h index 3d5c9095c5..7483c2d689 100644 --- a/src/MC/fix_bond_swap.h +++ b/src/MC/fix_bond_swap.h @@ -72,7 +72,8 @@ command-line option when running LAMMPS to see the offending line. E: Cannot use fix bond/swap with non-molecular systems -UNDOCUMENTED +Only systems with bonds that can be changed can be used. Atom_style +template does not qualify. E: Must use atom style with molecule IDs with fix bond/swap diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index aa2f370c16..9f7b45ae18 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -122,7 +122,7 @@ command-line option when running LAMMPS to see the offending line. E: Fix gcmc does not (yet) work with atom_style template -UNDOCUMENTED +Self-explanatory. E: Fix gcmc region does not support a bounding box @@ -195,10 +195,7 @@ enable the atom_modify first command. E: Fix gcmc ran out of available molecule IDs -This is a code limitation where more than MAXSMALLINT (usually around -two billion) molecules have been created. The code needs to be -modified to either allow molecule ID recycling or use bigger ints for -molecule IDs. A work-around is to run shorter simulations. +See the setting for tagint in the src/lmptype.h file. E: Fix gcmc could not find any atoms in the user-supplied template molecule diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h index 0eaffec9f3..3022f57180 100644 --- a/src/MISC/fix_deposit.h +++ b/src/MISC/fix_deposit.h @@ -77,7 +77,7 @@ command-line option when running LAMMPS to see the offending line. E: Invalid atom type in fix deposit command -UNDOCUMENTED +Self-explanatory. E: Must specify a region in fix deposit @@ -98,35 +98,39 @@ Self-explanatory. E: Cannot use fix_deposit unless atoms have IDs -UNDOCUMENTED +Self-explanatory. E: Fix deposit molecule must have coordinates -UNDOCUMENTED +The defined molecule does not specify coordinates. E: Fix deposit molecule must have atom types -UNDOCUMENTED +The defined molecule does not specify atom types. E: Invalid atom type in fix deposit mol command -UNDOCUMENTED +The atom types in the defined molecule are added to the value +specified in the create_atoms command, as an offset. The final value +for each atom must be between 1 to N, where N is the number of atom +types. -E: Fix deposit molecule template ID must be same as atom style template ID +E: Fix deposit molecule template ID must be same as atom_style template ID -UNDOCUMENTED +When using atom_style template, you cannot deposit molecules that are +not in that template. E: Cannot use fix deposit rigid and not molecule -UNDOCUMENTED +Self-explanatory. E: Cannot use fix deposit shake and not molecule -UNDOCUMENTED +Self-explanatory. E: Cannot use fix deposit rigid and shake -UNDOCUMENTED +These two attributes are conflicting. E: Region ID for fix deposit does not exist @@ -134,19 +138,19 @@ Self-explanatory. E: Fix pour rigid fix does not exist -UNDOCUMENTED +Self-explanatory. E: Fix deposit and fix rigid/small not using same molecule template ID -UNDOCUMENTED +Self-explanatory. E: Fix deposit shake fix does not exist -UNDOCUMENTED +Self-explanatory. E: Fix deposit and fix shake not using same molecule template ID -UNDOCUMENTED +Self-explanatory. W: Particle deposition was unsuccessful @@ -160,19 +164,15 @@ See the setting for bigint in the src/lmptype.h file. E: New atom IDs exceed maximum allowed ID -UNDOCUMENTED +See the setting for tagint in the src/lmptype.h file. E: Molecule template ID for fix deposit does not exist -UNDOCUMENTED +Self-explanatory. W: Molecule template for fix deposit has multiple molecules -UNDOCUMENTED - -U: Use of fix deposit with undefined lattice - -Must use lattice command with compute fix deposit command if units -option is set to lattice. +The fix deposit command will only create molecules of a single type, +i.e. the first molecule in the template. */ diff --git a/src/MISC/fix_efield.h b/src/MISC/fix_efield.h index ea31b3efe2..66f6074cf1 100644 --- a/src/MISC/fix_efield.h +++ b/src/MISC/fix_efield.h @@ -66,48 +66,46 @@ class FixEfield : public Fix { E: Illegal ... command -UNDOCUMENTED +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: Region ID for fix efield does not exist -UNDOCUMENTED +Self-explanatory. E: Fix efield requires atom attribute q or mu -UNDOCUMENTED +The atom style defined does not have this attribute. E: Variable name for fix efield does not exist -UNDOCUMENTED +Self-explanatory. E: Variable for fix efield is invalid style -UNDOCUMENTED +The variable must be an equal- or atom-style variable. E: Region ID for fix aveforce does not exist -UNDOCUMENTED +Self-explanatory. E: Fix efield with dipoles cannot use atom-style variables -UNDOCUMENTED +This option is not supported. W: The minimizer does not re-orient dipoles when using fix efield -UNDOCUMENTED +This means that only the atom coordinates will be minimized, +not the orientation of the dipoles. E: Cannot use variable energy with constant efield in fix efield -UNDOCUMENTED +LAMMPS computes the energy itself when the E-field is constant. E: Must use variable energy with fix efield -UNDOCUMENTED - -U: Neighbor list overflow, boost neigh_modify one - -There are too many neighbors of a single atom. Use the neigh_modify -command to increase the max number of neighbors allowed for one atom. -You may also want to boost the page size. +You must define an energy when performing a minimization with a +variable E-field. */ diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index 8b65c2aa49..51b66c2a43 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -72,12 +72,11 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) : if(strcmp(arg[7],"pprony") == 0) { series_type = 1; // series type 1 is 'positive Prony series' } else { - error->all(FLERR,"Fix gld series type must be pprony...for now"); + error->all(FLERR,"Fix gld series type must be pprony for now"); } // Error checking for the first set of required input arguments - if (seed <= 0) - error->all(FLERR,"Fix gld random seed must be > 0"); + if (seed <= 0) error->all(FLERR,"Illegal fix gld command"); if (prony_terms <= 0) error->all(FLERR,"Fix gld prony terms must be > 0"); if (t_start < 0) @@ -85,7 +84,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) : if (t_stop < 0) error->all(FLERR,"Fix gld stop temperature must be >= 0"); if (narg - narg_min < 2*(prony_terms) ) - error->all(FLERR,"Fix gld not enough prony series coefficients"); + error->all(FLERR,"Fix gld needs more prony series coefficients"); // allocate memory for Prony series force coefficients memory->create(prony_c, prony_terms, "gld:prony_c"); @@ -127,12 +126,13 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) : // optional arguments freezeflag = 0; zeroflag = 0; + while (iarg < narg) { if (strcmp(arg[iarg],"zero") == 0) { if (iarg+2 > narg) { error->all(FLERR, "Illegal fix gld command"); } - if (strcmp(arg[iarg+1],"no") == 0) { /* do nothing, default is zeroflag=0 */ } + if (strcmp(arg[iarg+1],"no") == 0) else if (strcmp(arg[iarg+1],"yes") == 0) { zeroflag = 1; } else { @@ -144,7 +144,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) : if (iarg+2 > narg) { error->all(FLERR, "Illegal fix gld command"); } - if (strcmp(arg[iarg+1],"no") == 0) { /* do nothing, default is unfrozen */ } + if (strcmp(arg[iarg+1],"no") == 0) else if (strcmp(arg[iarg+1],"yes") == 0) { freezeflag = 1; for (int i = 0; i < atom->nlocal; i++) { @@ -359,7 +359,7 @@ void FixGLD::initial_integrate(int vflag) // correct the random force, if zeroflag is set if (zeroflag) { count = group->count(igroup); - if (count == 0) error->all(FLERR,"Cannot zero gld force of 0 atoms"); + if (count == 0) error->all(FLERR,"Cannot zero gld force for zero atoms"); MPI_Allreduce(fsum,fsumall,3,MPI_DOUBLE,MPI_SUM,world); fsumall[0] /= (count*prony_terms); diff --git a/src/MISC/fix_gld.h b/src/MISC/fix_gld.h index 1b0e907f7c..4dbf9b3908 100644 --- a/src/MISC/fix_gld.h +++ b/src/MISC/fix_gld.h @@ -78,40 +78,36 @@ 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 gld series type must be pprony...for now +E: Fix gld series type must be pprony for now -UNDOCUMENTED - -E: Fix gld random seed must be > 0 - -UNDOCUMENTED +Self-explanatory. E: Fix gld prony terms must be > 0 -UNDOCUMENTED +Self-explanatory. E: Fix gld start temperature must be >= 0 -UNDOCUMENTED +Self-explanatory. E: Fix gld stop temperature must be >= 0 -UNDOCUMENTED +Self-explanatory. -E: Fix gld not enough prony series coefficients +E: Fix gld needs more prony series coefficients -UNDOCUMENTED +Self-explanatory. E: Fix gld c coefficients must be >= 0 -UNDOCUMENTED +Self-explanatory. E: Fix gld tau coefficients must be > 0 -UNDOCUMENTED +Self-explanatory. -E: Cannot zero gld force of 0 atoms +E: Cannot zero gld force for zero atoms -UNDOCUMENTED +There are no atoms currently in the group. */ diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h index 8c7e3d189f..df0d2c40dd 100644 --- a/src/POEMS/fix_poems.h +++ b/src/POEMS/fix_poems.h @@ -132,7 +132,7 @@ Self-explanatory. E: Too many molecules for fix poems -UNDOCUMENTED +The limit is 2^31 = ~2 billion molecules. E: No rigid bodies defined diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h index bc6a256550..8cd543e46a 100644 --- a/src/RIGID/fix_rigid.h +++ b/src/RIGID/fix_rigid.h @@ -160,7 +160,7 @@ Self-explanatory. E: Too many molecules for fix rigid -UNDOCUMENTED +The limit is 2^31 = ~2 billion molecules. E: Could not find fix rigid group ID @@ -208,7 +208,8 @@ incorrect. W: Cannot count rigid body degrees-of-freedom before bodies are fully initialized -UNDOCUMENTED +This means the temperature associated with the rigid bodies may be +incorrect on this timestep. W: Computing temperature of portions of rigid bodies @@ -241,7 +242,7 @@ A read operation from the file failed. E: Fix rigid file has no lines -UNDOCUMENTED +Self-explanatory. E: Incorrect rigid body format in fix rigid file @@ -254,6 +255,7 @@ that are defined by the fix rigid command. E: Cannot open fix rigid restart file %s -UNDOCUMENTED +The specified file cannot be opened. Check that the path and name are +correct. */ diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h index b5177fcaeb..04e61211ce 100644 --- a/src/RIGID/fix_rigid_small.h +++ b/src/RIGID/fix_rigid_small.h @@ -203,7 +203,7 @@ Self-explanatory. E: Fix rigid/small requires an atom map, see atom_modify -UNDOCUMENTED +Self-explanatory. E: Fix rigid/small langevin period must be > 0.0 @@ -211,19 +211,20 @@ Self-explanatory. E: Molecule template ID for fix rigid/small does not exist -UNDOCUMENTED +Self-explanatory. W: Molecule template for fix rigid/small has multiple molecules -UNDOCUMENTED +The fix rigid/small command will only recoginze molecules of a single +type, i.e. the first molecule in the template. E: Fix rigid/small molecule must have coordinates -UNDOCUMENTED +The defined molecule does not specify coordinates. E: Fix rigid/small molecule must have atom types -UNDOCUMENTED +The defined molecule does not specify atom types. W: More than one fix rigid @@ -237,7 +238,8 @@ incorrect. W: Cannot count rigid body degrees-of-freedom before bodies are fully initialized -UNDOCUMENTED +This means the temperature associated with the rigid bodies may be +incorrect on this timestep. W: Computing temperature of portions of rigid bodies @@ -261,42 +263,33 @@ are not within the required tolerances. E: Cannot open fix rigid/small infile %s -UNDOCUMENTED +The specified file cannot be opened. Check that the path and name are +correct. E: Unexpected end of fix rigid/small file -UNDOCUMENTED +A read operation from the file failed. E: Fix rigid file has no lines -UNDOCUMENTED +Self-explanatory. E: Incorrect rigid body format in fix rigid/small file -UNDOCUMENTED +The number of fields per line is not what expected. E: Invalid rigid body ID in fix rigid/small file -UNDOCUMENTED +The ID does not match the number or an existing ID of rigid bodies +that are defined by the fix rigid/small command. E: Cannot open fix rigid restart file %s -UNDOCUMENTED +The specified file cannot be opened. Check that the path and name are +correct. E: Rigid body atoms %ld %ld missing on proc %d at step %ld -UNDOCUMENTED - -U: Rigid body atoms missing on proc %d at step %ld - -UNDOCUMENTED - -U: No rigid bodies defined - -The fix specification did not end up defining any rigid bodies. - -U: Rigid body atoms %d %d missing on proc %d at step %ld - This means that an atom cannot find the atom that owns the rigid body it is part of, or vice versa. The solution is to use the communicate cutoff command to insure ghost atoms are acquired from far enough away diff --git a/src/RIGID/fix_shake.h b/src/RIGID/fix_shake.h index c0668ba74c..e35bb43eaa 100644 --- a/src/RIGID/fix_shake.h +++ b/src/RIGID/fix_shake.h @@ -167,15 +167,16 @@ types. E: Molecule template ID for fix shake does not exist -UNDOCUMENTED +Self-explanatory. W: Molecule template for fix shake has multiple molecules -UNDOCUMENTED +The fix shake command will only recoginze molecules of a single +type, i.e. the first molecule in the template. E: Fix shake molecule template must have shake info -UNDOCUMENTED +The defined molecule does not specify SHAKE information. E: More than one fix shake @@ -207,15 +208,21 @@ types for the 2 bonds in the angle. E: Shake atoms %ld %ld missing on proc %d at step %ld -UNDOCUMENTED +The 2 atoms in a single shake cluster specified by the fix shake +command are not all accessible to a processor. This probably means +an atom has moved too far. E: Shake atoms %ld %ld %ld missing on proc %d at step %ld -UNDOCUMENTED +The 3 atoms in a single shake cluster specified by the fix shake +command are not all accessible to a processor. This probably means +an atom has moved too far. E: Shake atoms %ld %ld %ld %ld missing on proc %d at step %ld -UNDOCUMENTED +The 4 atoms in a single shake cluster specified by the fix shake +command are not all accessible to a processor. This probably means +an atom has moved too far. E: Did not find fix shake partner info @@ -245,34 +252,4 @@ E: Shake determinant = 0.0 The determinant of the matrix being solved for a single cluster specified by the fix shake command is numerically invalid. -U: Shake atoms missing on proc %d at step %ld - -UNDOCUMENTED - -U: Shake atoms missing on proc %d at step %ld - -UNDOCUMENTED - -U: Shake atoms missing on proc %d at step %ld - -UNDOCUMENTED - -U: Shake atoms %d %d missing on proc %d at step %ld - -The 2 atoms in a single shake cluster specified by the fix shake -command are not all accessible to a processor. This probably means -an atom has moved too far. - -U: Shake atoms %d %d %d missing on proc %d at step %ld - -The 3 atoms in a single shake cluster specified by the fix shake -command are not all accessible to a processor. This probably means -an atom has moved too far. - -U: Shake atoms %d %d %d %d missing on proc %d at step %ld - -The 4 atoms in a single shake cluster specified by the fix shake -command are not all accessible to a processor. This probably means -an atom has moved too far. - */ diff --git a/src/SHOCK/fix_append_atoms.h b/src/SHOCK/fix_append_atoms.h index 2467b77c78..6343c42059 100644 --- a/src/SHOCK/fix_append_atoms.h +++ b/src/SHOCK/fix_append_atoms.h @@ -84,7 +84,9 @@ f_. E: Invalid basis setting in fix append/atoms command -UNDOCUMENTED +The basis index must be between 1 to N where N is the number of basis +atoms in the lattice. The type index must be between 1 to N where N +is the number of atom types. E: Cannot use append/atoms in periodic dimension @@ -104,8 +106,4 @@ E: Too many total atoms See the setting for bigint in the src/lmptype.h file. -U: Use of fix append/atoms with undefined lattice - -A lattice must be defined before using this fix. - */ diff --git a/src/compute.h b/src/compute.h index 0c96617d19..69bf3cda75 100644 --- a/src/compute.h +++ b/src/compute.h @@ -170,9 +170,7 @@ want. E: Too many molecules for compute -The compute molecule commands store a list of all molecules in the -system. The size of that list must fit in a 32-bit integer, i.e. be -less than ~2 billion molecules. +The limit is 2^31 = ~2 billion molecules. W: One or more compute molecules has atoms not in group diff --git a/src/create_box.h b/src/create_box.h index 1dd3e7a743..3675fbf856 100644 --- a/src/create_box.h +++ b/src/create_box.h @@ -57,8 +57,8 @@ Self-explanatory. E: Create_box region does not support a bounding box -Not all region styles define a bounding box which is required for use -with the create_box command. See the region command for details. +Not all regions represent bounded volumes. You cannot use +such a region with the create_box command. E: No bonds allowed with this atom style diff --git a/src/fix_ave_spatial.h b/src/fix_ave_spatial.h index c260d1e9ab..61116528cc 100644 --- a/src/fix_ave_spatial.h +++ b/src/fix_ave_spatial.h @@ -162,7 +162,8 @@ Self-explanatory. E: Fix ave/spatial settings invalid with changing box size -UNDOCUMENTED +If the box size changes, only the units reduced option can be +used. E: Fix for fix ave/spatial not computed at compatible time @@ -174,14 +175,4 @@ E: Fix ave/spatial missed timestep You cannot reset the timestep to a value beyond where the fix expects to next perform averaging. -U: Fix ave/spatial settings invalid with changing box - -If the ave setting is "running" or "window" and the box size/shape -changes during the simulation, then the units setting must be -"reduced", else the number of bins may change. - -U: Use of fix ave/spatial with undefined lattice - -A lattice must be defined to use fix ave/spatial with units = lattice. - */ diff --git a/src/fix_nve_limit.h b/src/fix_nve_limit.h index f22c8d4bda..aea1718f39 100644 --- a/src/fix_nve_limit.h +++ b/src/fix_nve_limit.h @@ -58,6 +58,6 @@ command-line option when running LAMMPS to see the offending line. W: Should not use fix nve/limit with fix shake -UNDOCUMENTED +This will lead to invalid constraint forces in the SHAKE computation. */ diff --git a/src/fix_property_atom.h b/src/fix_property_atom.h index c3d10ddc21..0a7fdcb57a 100644 --- a/src/fix_property_atom.h +++ b/src/fix_property_atom.h @@ -74,34 +74,36 @@ command-line option when running LAMMPS to see the offending line. E: Fix property/atom mol when atom_style already has molecule attribute -UNDOCUMENTED +Self-explanatory. E: Fix property/atom cannot specify mol twice -UNDOCUMENTED +Self-explanatory. E: Fix property/atom q when atom_style already has charge attribute -UNDOCUMENTED +Self-explanatory. E: Fix property/atom cannot specify q twice -UNDOCUMENTED +Self-explanatory. E: Fix property/atom vector name already exists -UNDOCUMENTED +The name for an integer or floating-point vector must be unique. E: Atom style was redefined after using fix property/atom -UNDOCUMENTED +This is not allowed. E: Incorrect %s format in data file -UNDOCUMENTED +A section of the data file being read by fix property/atom does +not have the correct number of values per line. E: Invalid atom ID in %s section of data file -UNDOCUMENTED +An atom in a section of the data file being read by fix property/atom +has an invalid atom ID that is <= 0 or > the maximum existing atom ID. */ diff --git a/src/fix_restrain.h b/src/fix_restrain.h index 6b77fb5751..8804e3c98c 100644 --- a/src/fix_restrain.h +++ b/src/fix_restrain.h @@ -88,14 +88,6 @@ atom has moved too far. W: Restrain problem: %d %ld %ld %ld %ld %ld -UNDOCUMENTED - -U: Restrain problem: %d %ld - -UNDOCUMENTED - -U: Restrain problem: %d %ld %d %d %d %d - Conformation of the 4 listed dihedral atoms is extreme; you may want to check your simulation geometry. diff --git a/src/fix_shear_history.h b/src/fix_shear_history.h index a0d7dfa940..15a7b6d932 100644 --- a/src/fix_shear_history.h +++ b/src/fix_shear_history.h @@ -80,7 +80,9 @@ cannot be tracked by the granular pair potential. E: Shear history overflow, boost neigh_modify one -UNDOCUMENTED +There are too many neighbors of a single atom. Use the neigh_modify +command to increase the max number of neighbors allowed for one atom. +You may also want to boost the page size. U: Too many touching neighbors - boost MAXTOUCH diff --git a/src/min_fire.cpp b/src/min_fire.cpp index aec66b85ae..6ef26e7eaa 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -86,7 +86,7 @@ int MinFire::iterate(int maxiter) bigint ntimestep; double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall; double scale1,scale2; - double dtvone,dtv,dtfm; + double dtvone,dtv,dtf,dtfm; int flag,flagall; alpha_final = 0.0; @@ -195,13 +195,15 @@ int MinFire::iterate(int maxiter) MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld); } + dtf = dtv * force->ftm2v; + // Euler integration step double **x = atom->x; if (rmass) { for (int i = 0; i < nlocal; i++) { - dtfm = dtv / rmass[i]; + dtfm = dtf / rmass[i]; x[i][0] += dtv * v[i][0]; x[i][1] += dtv * v[i][1]; x[i][2] += dtv * v[i][2]; @@ -211,7 +213,7 @@ int MinFire::iterate(int maxiter) } } else { for (int i = 0; i < nlocal; i++) { - dtfm = dtv / mass[type[i]]; + dtfm = dtf / mass[type[i]]; x[i][0] += dtv * v[i][0]; x[i][1] += dtv * v[i][1]; x[i][2] += dtv * v[i][2]; diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 04a33b6b23..46e418f6c7 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -82,7 +82,7 @@ int MinQuickMin::iterate(int maxiter) { bigint ntimestep; double vmax,vdotf,vdotfall,fdotf,fdotfall,scale; - double dtvone,dtv,dtfm; + double dtvone,dtv,dtf,dtfm; int flag,flagall; alpha_final = 0.0; @@ -162,13 +162,15 @@ int MinQuickMin::iterate(int maxiter) MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld); } + dtf = dtv * force->ftm2v; + // Euler integration step double **x = atom->x; if (rmass) { for (int i = 0; i < nlocal; i++) { - dtfm = dtv / rmass[i]; + dtfm = dtf / rmass[i]; x[i][0] += dtv * v[i][0]; x[i][1] += dtv * v[i][1]; x[i][2] += dtv * v[i][2]; @@ -178,7 +180,7 @@ int MinQuickMin::iterate(int maxiter) } } else { for (int i = 0; i < nlocal; i++) { - dtfm = dtv / mass[type[i]]; + dtfm = dtf / mass[type[i]]; x[i][0] += dtv * v[i][0]; x[i][1] += dtv * v[i][1]; x[i][2] += dtv * v[i][2];