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Merge pull request #1477 from jrgissing/bond/react-reaction_topology_overflow 

Implement fix bond/react reaction topology overflow checks
This commit is contained in:
Axel Kohlmeyer 2019-06-04 11:02:57 -04:00 committed by GitHub
parent 27cd78b96d 983f3adbb4
commit 47c6cd86f2
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6 changed files with 192 additions and 90 deletions
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56
doc/src/Errors_messages.txt
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@ -610,6 +610,62 @@ This means there is something invalid about the topology definitions. :dd
The data file header lists bonds but no bond types. :dd
{Bond/react: Cannot use fix bond/react with non-molecular systems} :dt
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify. :dd
{Bond/react: Rmax cutoff is longer than pairwise cutoff} :dt
This is not allowed because bond creation is done using the pairwise
neighbor list. :dd
{Bond/react: Molecule template ID for fix bond/react does not exist} :dt
A valid molecule template must have been created with the molecule
command. :dd
{Bond/react: Reaction templates must contain the same number of atoms} :dt
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file. :dd
{Bond/react: Unknown section in map file} :dt
Please ensure reaction map files are properly formatted. :dd
{Bond/react: Atom affected by reaction too close to template edge} :dt
This means an atom which changes type during the reaction is too close
to an 'edge' atom defined in the superimpose file. This could cause
incorrect assignment of bonds, angle, etc. Generally, this means you
must include more atoms in your templates, such that there are at
least two atoms between each atom involved in the reaction and an edge
atom. :dd
{Bond/react: Fix bond/react needs ghost atoms from farther away} :dt
This is because a processor needs to superimpose the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range. :dd
{Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted} :dt
Self-explanatory. :dd
{Bond/react special bond generation overflow} :dt
The number of special bonds per-atom created by a reaction exceeds the
system setting. See the read_data or create_box command for how to
specify this value. :dd
{Bond/react topology/atom exceed system topology/atom} :dt
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value. :dd
{Both restart files must use % or neither} :dt
Self-explanatory. :dd

5
doc/src/Errors_warnings.txt
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@ -82,6 +82,11 @@ bond/angle/dihedral. LAMMPS computes this by taking the maximum bond
length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch. :dd
{Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type} :dt
You may want to double-check that all atom types are properly assigned
in the post-reaction template. :dd
{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
Self-explanatory. :dd

71
doc/src/fix_bond_react.txt
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@ -18,8 +18,8 @@ fix ID group-ID bond/react common_keyword values ...
ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
bond/react = style name of this fix command :l
zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
these apply to all reaction specifications (below) :l
the common keyword/values may be appended directly after 'bond/react' :l
this applies to all reaction specifications (below) :l
common_keyword = {stabilization} :l
{stabilization} values = {no} or {yes} {group-ID} {xmax}
{no} = no reaction site stabilization
@ -136,10 +136,12 @@ words, can be customized for each reaction, or reaction step):
A check for possible new reaction sites is performed every {Nevery}
timesteps.
Two conditions must be met for a reaction to occur. First a bonding
atom pair must be identified. Second, the topology surrounding the
bonding atom pair must match the topology of the pre-reaction
template. If both these conditions are met, the reaction site is
Three physical conditions must be met for a reaction to occur. First,
a bonding atom pair must be identified within the reaction distance
cutoffs. Second, the topology surrounding the bonding atom pair must
match the topology of the pre-reaction template. Finally, any reaction
constraints listed in the map file (see below) must be satisfied. If
all of these conditions are met, the reaction site is eligible to be
modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
@ -203,14 +205,24 @@ new types must also be defined during the setup of a given simulation.
A discussion of correctly handling this is also provided on the
"molecule"_molecule.html command page.
NOTE: When a reaction occurs, it is possible that the resulting
topology/atom (e.g. special bonds, dihedrals, etc.) exceeds that of
the existing system and reaction templates. As when inserting
molecules, enough space for this increased topology/atom must be
reserved by using the relevant "extra" keywords to the
"read_data"_read_data.html or "create_box"_create_box.html commands.
The map file is a text document with the following format:
A map file has a header and a body. The header of map file the
contains one mandatory keyword and three optional keywords. The
mandatory keyword is 'equivalences' and the optional keywords are
'edgeIDs' and 'deleteIDs' and 'customIDs':
contains one mandatory keyword and four optional keywords. The
mandatory keyword is 'equivalences':
N {equivalences} = # of atoms N in the reaction molecule templates :pre
The optional keywords are 'edgeIDs', 'deleteIDs', 'customIDs' and
'constraints':
N {equivalences} = # of atoms N in the reaction molecule templates
N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
N {deleteIDs} = # of atoms N that are specified for deletion
N {customIDs} = # of atoms N that are specified for a custom update
@ -244,8 +256,8 @@ A sample map file is given below:
# this is a map file :pre
2 edgeIDs
7 equivalences :pre
7 equivalences
2 edgeIDs :pre
BondingIDs :pre
@ -297,26 +309,25 @@ can allow for the possibility of one or more reverse reactions.
The optional keywords deal with the probability of a given reaction
occurring as well as the stable equilibration of each reaction site as
it occurs.
it occurs:
The {prob} keyword can affect whether an eligible reaction actually
occurs. The fraction setting must be a value between 0.0 and 1.0. A
uniform random number between 0.0 and 1.0 is generated and the
The {prob} keyword can affect whether or not an eligible reaction
actually occurs. The fraction setting must be a value between 0.0 and
1.0. A uniform random number between 0.0 and 1.0 is generated and the
eligible reaction only occurs if the random number is less than the
fraction. Up to N reactions are permitted to occur, as optionally
specified by the {max_rxn} keyword.
The {stabilize_steps} keyword allows for the specification of how many
timesteps a reaction site is stabilized before being returned to the
overall system thermostat.
In order to produce the most physical behavior, this 'reaction site
equilibration time' should be tuned to be as small as possible while
retaining stability for a given system or reaction step. After a
limited number of case studies, this number has been set to a default
of 60 timesteps. Ideally, it should be individually tuned for each fix
reaction step. Note that in some situations, decreasing rather than
increasing this parameter will result in an increase in stability.
overall system thermostat. In order to produce the most physical
behavior, this 'reaction site equilibration time' should be tuned to
be as small as possible while retaining stability for a given system
or reaction step. After a limited number of case studies, this number
has been set to a default of 60 timesteps. Ideally, it should be
individually tuned for each fix reaction step. Note that in some
situations, decreasing rather than increasing this parameter will
result in an increase in stability.
The {update_edges} keyword can increase the number of atoms whose
atomic charges are updated, when the pre-reaction template contains
@ -324,11 +335,11 @@ edge atoms. When the value is set to 'charges,' all atoms' atomic
charges are updated to those specified by the post-reaction template,
including atoms near the edge of reaction templates. When the value is
set to 'custom,' an additional section must be included in the map
file that specifies whether to update charges, on a per-atom basis.
The format of this section is detailed above. Listing a pre-reaction
atom ID with a value of 'charges' will force the update of the atom's
charge, even if it is near a template edge. Atoms not near a template
edge are unaffected by this setting.
file that specifies whether or not to update charges, on a per-atom
basis. The format of this section is detailed above. Listing a
pre-reaction atom ID with a value of 'charges' will force the update
of the atom's charge, even if it is near a template edge. Atoms not
near a template edge are unaffected by this setting.
A few other considerations:

1
doc/utils/sphinx-config/false_positives.txt
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@ -2844,6 +2844,7 @@ unoptimized
unpadded
unphysical
unphysically
unreacted
unscaled
unsets
unsmoothed

79
src/USER-MISC/fix_bond_react.cpp
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@ -308,8 +308,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
onemol->check_attributes(0);
twomol->check_attributes(0);
if (onemol->natoms != twomol->natoms)
error->all(FLERR,"Post-reacted template must contain the same "
"number of atoms as the pre-reacted template");
error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms");
get_molxspecials();
read(i);
fclose(fp);
@ -324,7 +323,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
delete [] files;
if (atom->molecular != 1)
error->all(FLERR,"Cannot use fix bond/react with non-molecular systems");
error->all(FLERR,"Bond/react: Cannot use fix bond/react with non-molecular systems");
// check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors
// if so, we don't need non-bonded neighbor list
@ -472,17 +471,19 @@ FixBondReact::~FixBondReact()
delete [] guess_branch;
delete [] pioneer_count;
char **newarg;
newarg = new char*[2];
newarg[0] = master_group;
newarg[1] = (char *) "delete";
group->assign(2,newarg);
if (stabilization_flag == 1) {
newarg[0] = exclude_group;
if (group) {
char **newarg;
newarg = new char*[2];
newarg[0] = master_group;
newarg[1] = (char *) "delete";
group->assign(2,newarg);
delete [] exclude_group;
if (stabilization_flag == 1) {
newarg[0] = exclude_group;
group->assign(2,newarg);
delete [] exclude_group;
}
delete [] newarg;
}
delete [] newarg;
}
/* ---------------------------------------------------------------------- */
@ -663,7 +664,7 @@ void FixBondReact::init()
// check cutoff for iatomtype,jatomtype
for (int i = 0; i < nreacts; i++) {
if (force->pair == NULL || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
error->all(FLERR,"Fix bond/react cutoff is longer than pairwise cutoff");
error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff");
}
// need a half neighbor list, built every Nevery steps
@ -1172,7 +1173,7 @@ void FixBondReact::superimpose_algorithm()
// let's go ahead and catch the simplest of hangs
//if (hang_catch > onemol->natoms*4)
if (hang_catch > atom->nlocal*30) {
error->one(FLERR,"Excessive iteration of superimpose algorithm");
error->one(FLERR,"Bond/react: Excessive iteration of superimpose algorithm");
}
}
}
@ -1285,7 +1286,7 @@ void FixBondReact::make_a_guess()
for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) {
if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away1"); // parallel issues.
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away1"); // parallel issues.
}
if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) {
status = GUESSFAIL;
@ -1396,7 +1397,7 @@ void FixBondReact::check_a_neighbor()
//another check for ghost atoms. perhaps remove the one in make_a_guess
if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away2");
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away2");
}
for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) {
@ -1448,7 +1449,7 @@ void FixBondReact::check_a_neighbor()
//another check for ghost atoms. perhaps remove the one in make_a_guess
if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away3");
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away3");
}
for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) {
@ -1490,7 +1491,7 @@ void FixBondReact::crosscheck_the_neighbor()
glove[onemol_xspecial[pion][trace]-1][0] == 0) {
if (avail_guesses == MAXGUESS) {
error->warning(FLERR,"Fix bond/react failed because MAXGUESS set too small. ask developer for info");
error->warning(FLERR,"Bond/react: Fix bond/react failed because MAXGUESS set too small. ask developer for info");
status = GUESSFAIL;
return;
}
@ -1559,7 +1560,7 @@ void FixBondReact::inner_crosscheck_loop()
//another check for ghost atoms. perhaps remove the one in make_a_guess
if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away4");
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away4");
}
if (guess_branch[avail_guesses-1] == 0) avail_guesses--;
@ -1720,7 +1721,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// if atoms change types, but aren't landlocked, that's bad
for (int i = 0; i < twomol->natoms; i++) {
if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0)
error->one(FLERR,"Atom affected by reaction too close to template edge");
error->one(FLERR,"Bond/react: Atom affected by reaction too close to template edge");
}
// additionally, if a bond changes type, but neither involved atom is landlocked, bad
@ -1736,7 +1737,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
error->one(FLERR,"Bond type affected by reaction too close to template edge");
error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
}
}
}
@ -1746,7 +1747,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
if (onemol_batom == equivalences[i][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
error->one(FLERR,"Bond type affected by reaction too close to template edge");
error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
}
}
}
@ -1762,7 +1763,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
int ii = reverse_equiv[i][1][myrxn] - 1;
for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted");
error->one(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted");
}
}
}
@ -1773,7 +1774,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
for (int i = 0; i < twomol->natoms; i++) {
if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
char str[128];
sprintf(str,"An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
sprintf(str,"Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
error->warning(FLERR,str);
break;
}
@ -2261,7 +2262,7 @@ void FixBondReact::update_everything()
if (landlocked_atoms[j][rxnID] == 1) {
for (int k = 0; k < nspecial[atom->map(update_mega_glove[jj+1][i])][2]; k++) {
if (atom->map(special[atom->map(update_mega_glove[jj+1][i])][k]) < 0) {
error->all(FLERR,"Fix bond/react needs ghost atoms from further away - most likely too many processors");
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away - most likely too many processors");
}
}
}
@ -2322,6 +2323,8 @@ void FixBondReact::update_everything()
nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
}
if (nspecial[atom->map(update_mega_glove[jj+1][i])][2] > atom->maxspecial)
error->one(FLERR,"Bond/react special bond generation overflow");
for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) {
special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
}
@ -2383,6 +2386,8 @@ void FixBondReact::update_everything()
bond_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->bond_type[j][p];
bond_atom[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i];
num_bond[atom->map(update_mega_glove[jj+1][i])]++;
if (num_bond[atom->map(update_mega_glove[jj+1][i])] > atom->bond_per_atom)
error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
delta_bonds++;
}
}
@ -2457,6 +2462,8 @@ void FixBondReact::update_everything()
angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
num_angle[atom->map(update_mega_glove[jj+1][i])]++;
if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom)
error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
delta_angle++;
}
}
@ -2538,6 +2545,8 @@ void FixBondReact::update_everything()
dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
num_dihedral[atom->map(update_mega_glove[jj+1][i])]++;
if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom)
error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
delta_dihed++;
}
}
@ -2619,6 +2628,8 @@ void FixBondReact::update_everything()
improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
num_improper[atom->map(update_mega_glove[jj+1][i])]++;
if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom)
error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
delta_imprp++;
}
}
@ -2716,7 +2727,7 @@ void FixBondReact::read(int myrxn)
// skip 1st line of file
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of superimpose file");
if (eof == NULL) error->one(FLERR,"Bond/react: Unexpected end of superimpose file");
// read header lines
// skip blank lines or lines that start with "#"
@ -2770,7 +2781,7 @@ void FixBondReact::read(int myrxn)
DeleteAtoms(line, myrxn);
} else if (strcmp(keyword,"Constraints") == 0) {
Constraints(line, myrxn);
} else error->one(FLERR,"Unknown section in superimpose file");
} else error->one(FLERR,"Bond/react: Unknown section in map file");
parse_keyword(1,line,keyword);
@ -2778,13 +2789,13 @@ void FixBondReact::read(int myrxn)
// error check
if (bondflag == 0 || equivflag == 0)
error->all(FLERR,"Superimpose file missing BondingIDs or Equivalences section\n");
error->all(FLERR,"Bond/react: Map file missing BondingIDs or Equivalences section\n");
if (update_edges_flag[myrxn] == 2 && customedgesflag == 0)
error->all(FLERR,"Map file must have a Custom Edges section when using 'update_edges custom'\n");
error->all(FLERR,"Bond/react: Map file must have a Custom Edges section when using 'update_edges custom'\n");
if (update_edges_flag[myrxn] != 2 && customedgesflag == 1)
error->all(FLERR,"Specify 'update_edges custom' to include Custom Edges section in map file\n");
error->all(FLERR,"Bond/react: Specify 'update_edges custom' to include Custom Edges section in map file\n");
}
void FixBondReact::EdgeIDs(char *line, int myrxn)
@ -2830,7 +2841,7 @@ void FixBondReact::CustomEdges(char *line, int myrxn)
else if (strcmp(edgemode,"charges") == 0)
custom_edges[tmp-1][myrxn] = 1;
else
error->one(FLERR,"Illegal value in 'Custom Edges' section of map file");
error->one(FLERR,"Bond/react: Illegal value in 'Custom Edges' section of map file");
}
delete [] edgemode;
}
@ -2861,7 +2872,7 @@ void FixBondReact::Constraints(char *line, int myrxn)
constraints[myrxn][3] = tmp[2]*tmp[2]; // using square of distance
constraints[myrxn][4] = tmp[3]*tmp[3];
} else
error->one(FLERR,"Illegal constraint type in 'Constraints' section of map file");
error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file");
}
delete [] constraint_type;
}
@ -2871,7 +2882,7 @@ void FixBondReact::open(char *file)
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open superimpose file %s",file);
snprintf(str,128,"Bond/react: Cannot open map file %s",file);
error->one(FLERR,str);
}
}
@ -2884,7 +2895,7 @@ void FixBondReact::readline(char *line)
else n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
if (n == 0) error->all(FLERR,"Unexpected end of superimpose file");
if (n == 0) error->all(FLERR,"Bond/react: Unexpected end of map file");
MPI_Bcast(line,n,MPI_CHAR,0,world);
}

70
src/USER-MISC/fix_bond_react.h
View File

@ -189,47 +189,65 @@ 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: Invalid exclude group name
E: Bond/react: Cannot use fix bond/react with non-molecular systems
Exclude group name should not previously be defined.
E: Cannot use fix bond/react with non-molecular systems
Only systems with bonds that can be changed can be used. Atom_style
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
E: Fix bond/react cutoff is longer than pairwise cutoff
E: Bond/react: Rmax cutoff is longer than pairwise cutoff
This is not allowed because bond creation is done using the
pairwise neighbor list.
This is not allowed because bond creation is done using the pairwise
neighbor list.
E: Molecule template ID for fix bond/react does not exist
E: Bond/react: Molecule template ID for fix bond/react does not exist
A valid molecule template must have been created with the molecule command.
A valid molecule template must have been created with the molecule
command.
E: Superimpose file errors:
E: Bond/react: Reaction templates must contain the same number of atoms
Please ensure superimpose file is properly formatted.
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
E: Atom affected by reaction too close to template edge
E: Bond/react: Unknown section in map file
Please ensure reaction map files are properly formatted.
E: Bond/react: Atom affected by reaction too close to template edge
This means an atom which changes type during the reaction is too close
to an 'edge' atom defined in the superimpose file. This could cause incorrect
assignment of bonds, angle, etc. Generally, this means you must include
more atoms in your templates, such that there are at least two atoms
between each atom involved in the reaction and an edge atom.
to an 'edge' atom defined in the superimpose file. This could cause
incorrect assignment of bonds, angle, etc. Generally, this means you
must include more atoms in your templates, such that there are at
least two atoms between each atom involved in the reaction and an edge
atom.
E: Fix bond/react needs ghost atoms from farther away
E: Bond/react: Fix bond/react needs ghost atoms from farther away
This is because a processor needs to superimpose the entire unreacted
molecule template onto simulation atoms it can 'see.' The comm_modify cutoff
command can be used to extend the communication range.
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
E: Excessive iteration of superimpose algorithm
E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted
You may have discovered a bug! But first, please double check that your
molecule template atom types, bond types, etc. are consistent with your simulation,
and that all atoms affected by a reaction are sufficently separated from edge atoms.
If this issue persists, please contact the developer.
Self-explanatory.
W: Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type
You may want to double-check that all atom types are properly assigned
in the post-reaction template.
E: Bond/react special bond generation overflow
The number of special bonds per-atom created by a reaction exceeds the
system setting. See the read_data or create_box command for how to
specify this value.
E: Bond/react topology/atom exceed system topology/atom
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
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