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fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof

This commit is contained in:
Steve Plimpton 2017-03-23 15:31:27 -06:00
parent dcede304df
commit 44841f6891
42 changed files with 316 additions and 154 deletions
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21
doc/src/Section_howto.txt
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@ -1974,9 +1974,12 @@ The extract functions return a pointer to various global or per-atom
quantities stored in LAMMPS or to values calculated by a compute, fix,
or variable. The pointer returned by the extract_global() function
can be used as a permanent reference to a value which may change. For
the other extract functions, the underlying storage may be reallocated
as LAMMPS runs, so you need to re-call the function to assure a
current pointer or returned value(s).
the extract_atom() method, see the extract() method in the
src/atom.cpp file for a list of valid per-atom properties. New names
could easily be added if the property you want is not listed. For the
other extract functions, the underlying storage may be reallocated as
LAMMPS runs, so you need to re-call the function to assure a current
pointer or returned value(s).
The lammps_reset_box() function resets the size and shape of the
simulation box, e.g. as part of restoring a previously extracted and
@ -1992,11 +1995,15 @@ keyword as a double precision value.
The lammps_get_natoms() function returns the total number of atoms in
the system and can be used by the caller to allocate space for the
lammps_gather_atoms() and lammps_scatter_atoms() functions. The
gather function collects atom info of the requested type (atom coords,
types, forces, etc) from all processors, orders them by atom ID, and
returns a full list to each calling processor. The scatter function
does the inverse. It distributes the same kinds of values,
gather function collects peratom info of the requested type (atom
coords, types, forces, etc) from all processors, orders them by atom
ID, and returns a full list to each calling processor. The scatter
function does the inverse. It distributes the same peratom values,
passed by the caller, to each atom owned by individual processors.
Both methods are thus a means to extract or assign (overwrite) any
peratom quantities within LAMMPS. See the extract() method in the
src/atom.cpp file for a list of valid per-atom properties. New names
could easily be added if the property you want is not listed.
The lammps_create_atoms() function takes a list of N atoms as input
with atom types and coords (required), an optionally atom IDs and

50
doc/src/Section_python.txt
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@ -594,10 +594,10 @@ flag = lmp.set_variable(name,value) # set existing named string-style vari
value = lmp.get_thermo(name) # return current value of a thermo keyword
natoms = lmp.get_natoms() # total # of atoms as int
data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc
lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms from data, ordered by atom ID
lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc :pre
@ -656,10 +656,10 @@ argument.
For extract_atom(), a pointer to internal LAMMPS atom-based data is
returned, which you can use via normal Python subscripting. See the
extract() method in the src/atom.cpp file for a list of valid names.
Again, new names could easily be added. A pointer to a vector of
doubles or integers, or a pointer to an array of doubles (double **)
or integers (int **) is returned. You need to specify the appropriate
data type via the type argument.
Again, new names could easily be added if the property you want is not
listed. A pointer to a vector of doubles or integers, or a pointer to
an array of doubles (double **) or integers (int **) is returned. You
need to specify the appropriate data type via the type argument.
For extract_compute() and extract_fix(), the global, per-atom, or
local data calculated by the compute or fix can be accessed. What is
@ -689,12 +689,16 @@ specified group.
The get_natoms() method returns the total number of atoms in the
simulation, as an int.
The gather_atoms() method returns a ctypes vector of ints or doubles
as specified by type, of length count*natoms, for the property of all
the atoms in the simulation specified by name, ordered by count and
then by atom ID. The vector can be used via normal Python
subscripting. If atom IDs are not consecutively ordered within
LAMMPS, a None is returned as indication of an error.
The gather_atoms() method allows any per-atom property (coordinates,
velocities, etc) to be extracted from LAMMPS. It returns a ctypes
vector of ints or doubles as specified by type, of length
count*natoms, for the named property for all atoms in the simulation.
The data is ordered by count and then by atom ID. See the extract()
method in the src/atom.cpp file for a list of valid names. Again, new
names could easily be added if the property you want is missing. The
vector can be used via normal Python subscripting. If atom IDs are
not consecutively ordered within LAMMPS, a None is returned as
indication of an error.
Note that the data structure gather_atoms("x") returns is different
from the data structure returned by extract_atom("x") in four ways.
@ -711,14 +715,18 @@ assigning a new values to the extract_atom() array. To do this with
the gather_atoms() vector, you need to change values in the vector,
then invoke the scatter_atoms() method.
The scatter_atoms() method takes a vector of ints or doubles as
specified by type, of length count*natoms, for the property of all the
atoms in the simulation specified by name, ordered by bount and then
by atom ID. It uses the vector of data to overwrite the corresponding
properties for each atom inside LAMMPS. This requires LAMMPS to have
its "map" option enabled; see the "atom_modify"_atom_modify.html
command for details. If it is not, or if atom IDs are not
consecutively ordered, no coordinates are reset.
The scatter_atoms() method allows any per-atom property (coordinates,
velocities, etc) to be inserted into LAMMPS, overwriting the current
property. It takes a vector of ints or doubles as specified by type,
of length count*natoms, for the named property for all atoms in the
simulation. The data should be ordered by count and then by atom ID.
See the extract() method in the src/atom.cpp file for a list of valid
names. Again, new names could easily be added if the property you
want is missing. It uses the vector of data to overwrite the
corresponding properties for each atom inside LAMMPS. This requires
LAMMPS to have its "map" option enabled; see the
"atom_modify"_atom_modify.html command for details. If it is not, or
if atom IDs are not consecutively ordered, no coordinates are reset.
The array of coordinates passed to scatter_atoms() must be a ctypes
vector of ints or doubles, allocated and initialized something like
@ -734,7 +742,7 @@ x\[2\] = z coord of atom with ID 1
x\[3\] = x coord of atom with ID 2
...
x\[n3-1\] = z coord of atom with ID natoms
lmp.scatter_coords("x",1,3,x) :pre
lmp.scatter_atoms("x",1,3,x) :pre
Alternatively, you can just change values in the vector returned by
gather_atoms("x",1,3), since it is a ctypes vector of doubles.

46
doc/src/compute_modify.txt
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@ -14,27 +14,29 @@ compute_modify compute-ID keyword value ... :pre
compute-ID = ID of the compute to modify :ulb,l
one or more keyword/value pairs may be listed :l
keyword = {extra} or {dynamic} :l
{extra} value = N
keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l
{extra/dof} value = N
N = # of extra degrees of freedom to subtract
{dynamic} value = {yes} or {no}
yes/no = do or do not recompute the number of atoms contributing to the temperature :pre
{extra} syntax is identical to {extra/dof}, will be disabled at some point
{dynamic/dof} value = {yes} or {no}
yes/no = do or do not recompute the number of atoms contributing to the temperature
{dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre
:ule
[Examples:]
compute_modify myTemp extra 0
compute_modify newtemp dynamic yes extra 600 :pre
compute_modify myTemp extra/dof 0
compute_modify newtemp dynamic/dof yes extra/dof 600 :pre
[Description:]
Modify one or more parameters of a previously defined compute. Not
all compute styles support all parameters.
The {extra} keyword refers to how many degrees-of-freedom are
subtracted (typically from 3N) as a normalizing factor in a
temperature computation. Only computes that compute a temperature use
this option. The default is 2 or 3 for "2d or 3d
The {extra/dof} or {extra} keyword refers to how many
degrees-of-freedom are subtracted (typically from 3N) as a normalizing
factor in a temperature computation. Only computes that compute a
temperature use this option. The default is 2 or 3 for "2d or 3d
systems"_dimension.html which is a correction factor for an ensemble
of velocities with zero total linear momentum. For compute
temp/partial, if one or more velocity components are excluded, the
@ -43,14 +45,18 @@ number for the {extra} parameter if you need to add
degrees-of-freedom. See the "compute
temp/asphere"_compute_temp_asphere.html command for an example.
The {dynamic} keyword determines whether the number of atoms N in the
compute group is re-computed each time a temperature is computed.
Only compute styles that calculate a temperature use this option. By
default, N is assumed to be constant. If you are adding atoms to the
system (see the "fix pour"_fix_pour.html or "fix
deposit"_fix_deposit.html commands) or expect atoms to be lost
(e.g. due to evaporation), then this option should be used to insure
the temperature is correctly normalized.
The {dynamic/dof} or {dynamic} keyword determines whether the number
of atoms N in the compute group is re-computed each time a temperature
is computed. Only compute styles that calculate a temperature use
this option. By default, N is assumed to be constant. If you are
adding atoms to the system (see the "fix pour"_fix_pour.html, "fix
deposit"_fix_deposit.html and "fix gcmc"_fix_gcmc.html commands) or
expect atoms to be lost (e.g. due to evaporation), then this option
should be used to insure the temperature is correctly normalized.
NOTE: The {extra} and {dynamic} keywords should not be used as they
are deprecated (March 2017) and will eventually be disabled. Instead,
use the equivalent {extra/dof} and {dynamic/dof} keywords.
[Restrictions:] none
@ -60,5 +66,5 @@ the temperature is correctly normalized.
[Default:]
The option defaults are extra = 2 or 3 for 2d or 3d systems and
dynamic = no.
The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
dynamic/dof = no.

15
doc/src/compute_sna_atom.txt
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@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
w_1, w_2,... = list of neighbor weights, one for each type :l
zero or more keyword/value pairs may be appended :l
keyword = {diagonal} or {rmin0} or {switchflag} :l
keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} :l
{diagonal} value = {0} or {1} or {2} or {3}
{0} = all j1, j2, j <= twojmax, j2 <= j1
{1} = subset satisfying j1 == j2
@ -33,7 +33,10 @@ keyword = {diagonal} or {rmin0} or {switchflag} :l
{rmin0} value = parameter in distance to angle conversion (distance units)
{switchflag} value = {0} or {1}
{0} = do not use switching function
{1} = use switching function :pre
{1} = use switching function
{bzeroflag} value = {0} or {1}
{0} = do not subtract B0
{1} = subtract B0 :pre
:ule
[Examples:]
@ -153,6 +156,12 @@ ordered in which they are listed
The keyword {switchflag} can be used to turn off the switching
function.
The keyword {bzeroflag} determines whether or not {B0}, the bispectrum
components of an atom with no neighbors, are subtracted from
the calculated bispectrum components. This optional keyword is only
available for compute {sna/atom}, as {snad/atom} and {snav/atom}
are unaffected by the removal of constant terms.
NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
@ -222,7 +231,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Default:]
The optional keyword defaults are {diagonal} = 0, {rmin0} = 0,
{switchflag} = 1.
{switchflag} = 1, {bzeroflag} = 0.
:line

6
doc/src/fix_deposit.txt
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@ -150,6 +150,12 @@ treated as rigid bodies, use the {rigid} keyword, specifying as its
value the ID of a separate "fix rigid/small"_fix_rigid.html
command which also appears in your input script.
NOTE: If you wish the new rigid molecules (and other rigid molecules)
to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
"fix_modify dynamic/dof yes" command for the rigid fix. This is to
inform that fix that the molecule count will vary dynamically.
If you wish to insert molecules via the {mol} keyword, that will have
their bonds or angles constrained via SHAKE, use the {shake} keyword,
specifying as its value the ID of a separate "fix

17
doc/src/fix_gcmc.txt
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@ -26,6 +26,8 @@ zero or more keyword/value pairs may be appended to args :l
keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, {tfac_insert}, or {overlap_cutoff}
{mol} value = template-ID
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
{rigid} value = fix-ID
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
{shake} value = fix-ID
fix-ID = ID of "fix shake"_fix_shake.html command
{region} value = region-ID
@ -161,6 +163,17 @@ soon generate an error when it tries to find bonded neighbors. LAMMPS will
warn you if any of the atoms eligible for deletion have a non-zero
molecule ID, but does not check for this at the time of deletion.
If you wish to insert molecules via the {mol} keyword, that will be
treated as rigid bodies, use the {rigid} keyword, specifying as its
value the ID of a separate "fix rigid/small"_fix_rigid.html
command which also appears in your input script.
NOTE: If you wish the new rigid molecules (and other rigid molecules)
to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
"fix_modify dynamic/dof yes" command for the rigid fix. This is to
inform that fix that the molecule count will vary dynamically.
If you wish to insert molecules via the {mol} keyword, that will have
their bonds or angles constrained via SHAKE, use the {shake} keyword,
specifying as its value the ID of a separate "fix
@ -343,10 +356,6 @@ may no longer exist since it might have been deleted by the first
fix gcmc command. An existing template molecule will need to be
referenced by the user for each subsequent fix gcmc command.
Because molecule insertion does not work in combination with
fix rigid, simulataneous use of fix rigid or fix rigid/small
with this fix is not allowed.
[Related commands:]
"fix atom/swap"_fix_atom_swap.html,

27
doc/src/fix_modify.txt
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@ -14,11 +14,13 @@ fix_modify fix-ID keyword value ... :pre
fix-ID = ID of the fix to modify :ulb,l
one or more keyword/value pairs may be appended :l
keyword = {temp} or {press} or {energy} or {respa} :l
keyword = {temp} or {press} or {energy} or {respa} or {dynamic/dof} :l
{temp} value = compute ID that calculates a temperature
{press} value = compute ID that calculates a pressure
{energy} value = {yes} or {no}
{respa} value = {1} to {max respa level} or {0} (for outermost level) :pre
{respa} value = {1} to {max respa level} or {0} (for outermost level)
{dynamic/dof} value = {yes} or {no}
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
:ule
[Examples:]
@ -78,6 +80,27 @@ enabled to support this feature; if not, {fix_modify} will report an
error. Active fixes with a custom RESPA level setting are reported
with their specified level at the beginning of a r-RESPA run.
The {dynamic/dof} keyword determines whether the number of atoms N in
the fix group and their associated degrees of freedom are re-computed
each time a temperature is computed. Only fix styles that calculate
their own internal temperature use this option. Currently this is
only the "fix rigid/nvt/small"_fix_rigid.html and "fix
rigid/npt/small"_fix_rigid.html commands for the purpose of
thermostatting rigid body translation and rotation. By default, N and
their DOF are assumed to be constant. If you are adding atoms or
molecules to the system (see the "fix pour"_fix_pour.html, "fix
deposit"_fix_deposit.html, and "fix gcmc"_fix_gcmc.html commands) or
expect atoms or molecules to be lost (e.g. due to exiting the
simulation box or via "fix evaporation"_fix_evaporation.html), then
this option should be used to insure the temperature is correctly
normalized.
NOTE: Other thermostatting fixes, such as "fix nvt"_fix_nh.html, do
not use the {dynamic/dof} keyword because they use a temperature
compute to calculate temperature. See the "compute_modify
dynamic/dof"_compute_modify.html command for a similar way to insure
correct temperature normalization for those thermostats.
[Restrictions:] none
[Related commands:]

6
doc/src/fix_pour.txt
View File

@ -117,6 +117,12 @@ treated as rigid bodies, use the {rigid} keyword, specifying as its
value the ID of a separate "fix rigid/small"_fix_rigid.html
command which also appears in your input script.
NOTE: If you wish the new rigid molecules (and other rigid molecules)
to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
"fix_modify dynamic/dof yes" command for the rigid fix. This is to
inform that fix that the molecule count will vary dynamically.
If you wish to insert molecules via the {mol} keyword, that will have
their bonds or angles constrained via SHAKE, use the {shake} keyword,
specifying as its value the ID of a separate "fix

5
doc/src/pair_snap.txt
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@ -131,14 +131,15 @@ The SNAP parameter file can contain blank and comment lines (start
with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are {rcutfac} and
{twojmax}. Optional keywords are {rfac0}, {rmin0}, {diagonalstyle},
and {switchflag}.
{switchflag}, and {bzeroflag}.
The default values for these keywords are
{rfac0} = 0.99363
{rmin0} = 0.0
{diagonalstyle} = 3
{switchflag} = 0 :ul
{switchflag} = 0
{bzeroflag} = 1 :ul
Detailed definitions of these keywords are given on the "compute
sna/atom"_compute_sna_atom.html doc page.

4
examples/accelerate/in.lc
View File

@ -30,7 +30,7 @@ set group all quat/random 982381
compute rot all temp/asphere
group spheroid type 1
variable dof equal count(spheroid)+3
compute_modify rot extra ${dof}
compute_modify rot extra/dof ${dof}
velocity all create 2.4 41787 loop geom
@ -45,7 +45,7 @@ thermo 100
# equilibration run
fix 1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra/dof ${dof}
run 200
# dynamics run

2
examples/deposit/in.deposit.atom
View File

@ -23,7 +23,7 @@ region mobile block 0 5 0 5 2 INF
group mobile region mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
compute_modify add dynamic/dof yes extra/dof 0
fix 1 addatoms nve
fix 2 mobile langevin 1.0 1.0 0.1 587283

2
examples/deposit/in.deposit.molecule
View File

@ -26,7 +26,7 @@ region mobile block 0 5 0 5 2 INF
group mobile region mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
compute_modify add dynamic/dof yes extra/dof 0
fix 1 addatoms nve
fix 2 mobile langevin 0.1 0.1 0.1 587283

2
examples/deposit/in.deposit.molecule.shake
View File

@ -26,7 +26,7 @@ region mobile block 0 5 0 5 2 INF
group mobile region mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
compute_modify add dynamic/dof yes extra/dof 0
fix 1 addatoms nve
fix 2 mobile langevin 0.1 0.1 0.1 587283

4
examples/ellipse/in.ellipse.gayberne
View File

@ -19,7 +19,7 @@ set group all quat/random 18238
compute rot all temp/asphere
group spheroid type 1
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra/dof ${dof}
velocity all create 2.4 87287 loop geom
@ -52,7 +52,7 @@ fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra/dof ${dof}
# equilibrate to shrink box around dilute system

4
examples/ellipse/in.ellipse.resquared
View File

@ -19,7 +19,7 @@ set group all quat/random 18238
compute rot all temp/asphere
group spheroid type 1
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra/dof ${dof}
velocity all create 2.4 87287 loop geom
@ -52,7 +52,7 @@ fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra/dof ${dof}
# equilibrate to shrink box around dilute system

6
examples/granregion/in.granregion.box
View File

@ -29,15 +29,15 @@ fix ins all pour 100 2 4767548 vol 0.4 10 &
timestep 0.005
compute 1 all temp
compute_modify 1 dynamic yes
compute_modify 1 dynamic/dof yes
compute 2 all temp/sphere
compute_modify 2 dynamic yes
compute_modify 2 dynamic/dof yes
thermo 100
thermo_style custom step atoms temp c_1 c_2 press
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
compute_modify thermo_temp dynamic/dof yes
#dump 2 all image 100 image.*.jpg type type &
# zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03

2
examples/pour/in.pour
View File

@ -33,7 +33,7 @@ compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 1000 dump.pour

2
examples/pour/in.pour.2d
View File

@ -39,7 +39,7 @@ compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 250 dump.pour

2
examples/pour/in.pour.2d.molecule
View File

@ -46,7 +46,7 @@ compute 1 all erotate/sphere
compute Tsphere all temp/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify lost ignore norm no temp Tsphere
compute_modify Tsphere dynamic yes
compute_modify Tsphere dynamic/dof yes
thermo 1000

1
examples/snap/Ta06A.snapparam
View File

@ -12,3 +12,4 @@ gamma 1
rfac0 0.99363
rmin0 0
diagonalstyle 3
bzeroflag 0

1
examples/snap/W_2940_2017_2.snapparam
View File

@ -10,3 +10,4 @@ gamma 1
rfac0 0.99363
rmin0 0
diagonalstyle 3
bzeroflag 0

63
src/MC/fix_gcmc.cpp
View File

@ -60,7 +60,7 @@ using namespace MathConst;
// this must be lower than MAXENERGYSIGNAL
// by a large amount, so that it is still
// less than total energy when negative
// energy changes are adddd to MAXENERGYSIGNAL
// energy changes are added to MAXENERGYSIGNAL
#define MAXENERGYTEST 1.0e50
@ -72,7 +72,7 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
idregion(NULL), full_flag(0), ngroups(0), groupstrings(NULL), ngrouptypes(0), grouptypestrings(NULL),
grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), atom_coord(NULL), random_equal(NULL), random_unequal(NULL),
coords(NULL), imageflags(NULL), idshake(NULL)
coords(NULL), imageflags(NULL), idrigid(NULL), idshake(NULL), fixrigid(NULL), fixshake(NULL)
{
if (narg < 11) error->all(FLERR,"Illegal fix gcmc command");
@ -182,8 +182,12 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
if (charge_flag && atom->q == NULL)
error->all(FLERR,"Fix gcmc atom has charge, but atom style does not");
if (rigidflag && mode == ATOM)
error->all(FLERR,"Cannot use fix gcmc rigid and not molecule");
if (shakeflag && mode == ATOM)
error->all(FLERR,"Cannot use fix gcmc shake and not molecule");
if (rigidflag && shakeflag)
error->all(FLERR,"Cannot use fix gcmc rigid and shake");
// setup of coords and imageflags array
@ -241,11 +245,11 @@ void FixGCMC::options(int narg, char **arg)
pressure_flag = false;
pressure = 0.0;
fugacity_coeff = 1.0;
rigidflag = 0;
shakeflag = 0;
charge = 0.0;
charge_flag = false;
full_flag = false;
idshake = NULL;
ngroups = 0;
int ngroupsmax = 0;
groupstrings = NULL;
@ -302,6 +306,14 @@ void FixGCMC::options(int narg, char **arg)
charge = force->numeric(FLERR,arg[iarg+1]);
charge_flag = true;
iarg += 2;
} else if (strcmp(arg[iarg],"rigid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
int n = strlen(arg[iarg+1]) + 1;
delete [] idrigid;
idrigid = new char[n];
strcpy(idrigid,arg[iarg+1]);
rigidflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"shake") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
int n = strlen(arg[iarg+1]) + 1;
@ -374,6 +386,7 @@ FixGCMC::~FixGCMC()
memory->destroy(coords);
memory->destroy(imageflags);
delete [] idrigid;
delete [] idshake;
if (ngroups > 0) {
@ -477,6 +490,21 @@ void FixGCMC::init()
"Fix gcmc molecule command requires that "
"atoms have molecule attributes");
// if rigidflag defined, check for rigid/small fix
// its molecule template must be same as this one
fixrigid = NULL;
if (rigidflag) {
int ifix = modify->find_fix(idrigid);
if (ifix < 0) error->all(FLERR,"Fix gcmc rigid fix does not exist");
fixrigid = modify->fix[ifix];
int tmp;
if (onemols != (Molecule **) fixrigid->extract("onemol",tmp))
error->all(FLERR,
"Fix gcmc and fix rigid/small not using "
"same molecule template ID");
}
// if shakeflag defined, check for SHAKE fix
// its molecule template must be same as this one
@ -491,13 +519,6 @@ void FixGCMC::init()
"same molecule template ID");
}
// check for fix rigid
for (int irigid = 0; irigid < modify->nfix; irigid++) {
if (strncmp(modify->fix[irigid]->style,"rigid",5) == 0)
error->all(FLERR,"Fix gcmc can not currently be used with any rigid fix");
}
if (domain->dimension == 2)
error->all(FLERR,"Cannot use fix gcmc in a 2d simulation");
@ -1353,10 +1374,15 @@ void FixGCMC::attempt_molecule_insertion()
modify->create_attribute(m);
}
}
if (shakeflag)
// FixRigidSmall::set_molecule stores rigid body attributes
// FixShake::set_molecule stores shake info for molecule
if (rigidflag)
fixrigid->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
@ -2011,7 +2037,12 @@ void FixGCMC::attempt_molecule_insertion_full()
}
}
if (shakeflag)
// FixRigidSmall::set_molecule stores rigid body attributes
// FixShake::set_molecule stores shake info for molecule
if (rigidflag)
fixrigid->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
else if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
@ -2095,7 +2126,7 @@ double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord)
int jtype = type[j];
// if overlap check requested, if overlap,
// return signal value = MAXENERGYSIGNAL
// return signal value for energy
if (overlap_flag && rsq < overlap_cutoff)
return MAXENERGYSIGNAL;
@ -2145,7 +2176,7 @@ double FixGCMC::energy_full()
int vflag = 0;
// if overlap check requested, if overlap,
// return signal value = MAXENERGYSIGNAL
// return signal value for energy
if (overlap_flag) {
double delx,dely,delz,rsq;

6
src/MC/fix_gcmc.h
View File

@ -128,9 +128,9 @@ class FixGCMC : public Fix {
int imol,nmol;
double **coords;
imageint *imageflags;
class Fix *fixshake;
int shakeflag;
char *idshake;
class Fix *fixrigid, *fixshake;
int rigidflag, shakeflag;
char *idrigid, *idshake;
int triclinic; // 0 = orthog box, 1 = triclinic
class Compute *c_pe;

2
src/MISC/fix_deposit.cpp
View File

@ -234,7 +234,7 @@ void FixDeposit::init()
fixrigid = NULL;
if (rigidflag) {
int ifix = modify->find_fix(idrigid);
if (ifix < 0) error->all(FLERR,"Fix pour rigid fix does not exist");
if (ifix < 0) error->all(FLERR,"Fix deposit rigid fix does not exist");
fixrigid = modify->fix[ifix];
int tmp;
if (onemols != (Molecule **) fixrigid->extract("onemol",tmp))

68
src/RIGID/fix_rigid_nh_small.cpp
View File

@ -321,36 +321,8 @@ void FixRigidNHSmall::init()
void FixRigidNHSmall::setup(int vflag)
{
FixRigidSmall::setup(vflag);
// total translational and rotational degrees of freedom
nf_t = dimension * nlocal_body;
if (dimension == 3) {
nf_r = dimension * nlocal_body;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
for (int k = 0; k < dimension; k++)
if (fabs(b->inertia[k]) < EPSILON) nf_r--;
}
} else if (dimension == 2) {
nf_r = nlocal_body;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
if (fabs(b->inertia[2]) < EPSILON) nf_r--;
}
}
double nf[2], nfall[2];
nf[0] = nf_t;
nf[1] = nf_r;
MPI_Allreduce(nf,nfall,2,MPI_DOUBLE,MPI_SUM,world);
nf_t = nfall[0];
nf_r = nfall[1];
g_f = nf_t + nf_r;
onednft = 1.0 + (double)(dimension) / (double)g_f;
onednfr = (double) (dimension) / (double)g_f;
compute_dof();
double mbody[3];
akin_t = akin_r = 0.0;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
@ -608,6 +580,7 @@ void FixRigidNHSmall::initial_integrate(int vflag)
if (tstat_flag) {
compute_temp_target();
if (dynamic) compute_dof();
nhc_temp_integrate();
}
@ -1273,6 +1246,40 @@ void FixRigidNHSmall::nh_epsilon_dot()
mtk_term2 /= g_f;
}
/* ---------------------------------------------------------------------- */
void FixRigidNHSmall::compute_dof()
{
// total translational and rotational degrees of freedom
nf_t = dimension * nlocal_body;
if (dimension == 3) {
nf_r = dimension * nlocal_body;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
for (int k = 0; k < dimension; k++)
if (fabs(b->inertia[k]) < EPSILON) nf_r--;
}
} else if (dimension == 2) {
nf_r = nlocal_body;
for (int ibody = 0; ibody < nlocal_body; ibody++) {
Body *b = &body[ibody];
if (fabs(b->inertia[2]) < EPSILON) nf_r--;
}
}
double nf[2], nfall[2];
nf[0] = nf_t;
nf[1] = nf_r;
MPI_Allreduce(nf,nfall,2,MPI_DOUBLE,MPI_SUM,world);
nf_t = nfall[0];
nf_r = nfall[1];
g_f = nf_t + nf_r;
onednft = 1.0 + (double)(dimension) / (double)g_f;
onednfr = (double) (dimension) / (double)g_f;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
@ -1508,4 +1515,3 @@ void FixRigidNHSmall::deallocate_order()
delete [] wdti2;
delete [] wdti4;
}

3
src/RIGID/fix_rigid_nh_small.h
View File

@ -78,7 +78,8 @@ class FixRigidNHSmall : public FixRigidSmall {
virtual void compute_temp_target();
void compute_press_target();
void nh_epsilon_dot();
void compute_dof();
void allocate_chain();
void allocate_order();
void deallocate_chain();

12
src/SNAP/compute_sna_atom.cpp
View File

@ -34,7 +34,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
radelem(NULL), wjelem(NULL)
{
double rmin0, rfac0;
int twojmax, switchflag;
int twojmax, switchflag, bzeroflag;
radelem = NULL;
wjelem = NULL;
@ -48,6 +48,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
diagonalstyle = 0;
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 0;
// offset by 1 to match up with types
@ -100,19 +101,24 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute sna/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"bzeroflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/atom command");
bzeroflag = atoi(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal compute sna/atom command");
}
snaptr = new SNA*[comm->nthreads];
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag)
#endif
{
int tid = omp_get_thread_num();
// always unset use_shared_arrays since it does not work with computes
snaptr[tid] = new SNA(lmp,rfac0,twojmax,diagonalstyle,
0 /*use_shared_arrays*/, rmin0,switchflag);
0 /*use_shared_arrays*/, rmin0,switchflag,bzeroflag);
}
ncoeff = snaptr[0]->ncoeff;

9
src/SNAP/compute_snad_atom.cpp
View File

@ -34,7 +34,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
radelem(NULL), wjelem(NULL)
{
double rfac0, rmin0;
int twojmax, switchflag;
int twojmax, switchflag, bzeroflag;
radelem = NULL;
wjelem = NULL;
@ -48,7 +48,8 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
diagonalstyle = 0;
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 0;
// process required arguments
memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types
memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
@ -98,14 +99,14 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
snaptr = new SNA*[comm->nthreads];
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag)
#endif
{
int tid = omp_get_thread_num();
// always unset use_shared_arrays since it does not work with computes
snaptr[tid] = new SNA(lmp,rfac0,twojmax,diagonalstyle,
0 /*use_shared_arrays*/, rmin0,switchflag);
0 /*use_shared_arrays*/, rmin0,switchflag,bzeroflag);
}
ncoeff = snaptr[0]->ncoeff;

7
src/SNAP/compute_snav_atom.cpp
View File

@ -34,7 +34,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
radelem(NULL), wjelem(NULL)
{
double rfac0, rmin0;
int twojmax, switchflag;
int twojmax, switchflag, bzeroflag;
radelem = NULL;
wjelem = NULL;
@ -50,6 +50,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
diagonalstyle = 0;
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 0;
// process required arguments
memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types
@ -100,14 +101,14 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
snaptr = new SNA*[comm->nthreads];
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag)
#pragma omp parallel default(none) shared(lmp,rfac0,twojmax,rmin0,switchflag,bzeroflag)
#endif
{
int tid = omp_get_thread_num();
// always unset use_shared_arrays since it does not work with computes
snaptr[tid] = new SNA(lmp,rfac0,twojmax,diagonalstyle,
0 /*use_shared_arrays*/, rmin0,switchflag);
0 /*use_shared_arrays*/, rmin0,switchflag,bzeroflag);
}
ncoeff = snaptr[0]->ncoeff;

5
src/SNAP/pair_snap.cpp
View File

@ -1411,7 +1411,7 @@ void PairSNAP::coeff(int narg, char **arg)
int tid = omp_get_thread_num();
sna[tid] = new SNA(lmp,rfac0,twojmax,
diagonalstyle,use_shared_arrays,
rmin0,switchflag);
rmin0,switchflag,bzeroflag);
if (!use_shared_arrays)
sna[tid]->grow_rij(nmax);
}
@ -1635,6 +1635,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
rmin0 = 0.0;
diagonalstyle = 3;
switchflag = 1;
bzeroflag = 0;
// open SNAP parameter file on proc 0
FILE *fpparam;
@ -1697,6 +1698,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
diagonalstyle = atoi(keyval);
else if (strcmp(keywd,"switchflag") == 0)
switchflag = atoi(keyval);
else if (strcmp(keywd,"bzeroflag") == 0)
bzeroflag = atoi(keyval);
else
error->all(FLERR,"Incorrect SNAP parameter file");
}

2
src/SNAP/pair_snap.h
View File

@ -98,7 +98,7 @@ protected:
double *wjelem; // elements weights
double **coeffelem; // element bispectrum coefficients
int *map; // mapping from atom types to elements
int twojmax, diagonalstyle, switchflag;
int twojmax, diagonalstyle, switchflag, bzeroflag;
double rcutfac, rfac0, rmin0, wj1, wj2;
int rcutfacflag, twojmaxflag; // flags for required parameters
int gammaoneflag; // 1 if parameter gamma is 1

29
src/SNAP/sna.cpp
View File

@ -115,14 +115,15 @@ using namespace MathConst;
SNA::SNA(LAMMPS* lmp, double rfac0_in,
int twojmax_in, int diagonalstyle_in, int use_shared_arrays_in,
double rmin0_in, int switch_flag_in) : Pointers(lmp)
double rmin0_in, int switch_flag_in, int bzero_flag_in) : Pointers(lmp)
{
wself = 1.0;
use_shared_arrays = use_shared_arrays_in;
rfac0 = rfac0_in;
rmin0 = rmin0_in;
switch_flag = switch_flag_in;
bzero_flag = bzero_flag_in;
twojmax = twojmax_in;
diagonalstyle = diagonalstyle_in;
@ -142,6 +143,12 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in,
nmax = 0;
idxj = NULL;
if (bzero_flag) {
double www = wself*wself*wself;
for(int j = 0; j <= twojmax; j++)
bzero[j] = www*(j+1);
}
#ifdef TIMING_INFO
timers = new double[20];
for(int i = 0; i < 20; i++) timers[i] = 0;
@ -151,6 +158,7 @@ SNA::SNA(LAMMPS* lmp, double rfac0_in,
build_indexlist();
}
/* ---------------------------------------------------------------------- */
@ -539,13 +547,11 @@ void SNA::compute_bi()
j <= MIN(twojmax, j1 + j2); j += 2) {
barray[j1][j2][j] = 0.0;
for(int mb = 0; 2*mb < j; mb++) {
for(int ma = 0; ma <= j; ma++) {
for(int mb = 0; 2*mb < j; mb++)
for(int ma = 0; ma <= j; ma++)
barray[j1][j2][j] +=
uarraytot_r[j][ma][mb] * zarray_r[j1][j2][j][ma][mb] +
uarraytot_i[j][ma][mb] * zarray_i[j1][j2][j][ma][mb];
}
}
// For j even, special treatment for middle column
@ -562,6 +568,8 @@ void SNA::compute_bi()
}
barray[j1][j2][j] *= 2.0;
if (bzero_flag)
barray[j1][j2][j] -= bzero[j];
}
}
@ -1512,6 +1520,12 @@ void SNA::create_twojmax_arrays()
memory->create(uarray_i, jdim, jdim, jdim,
"sna:uarray");
if (bzero_flag)
memory->create(bzero, jdim,"sna:bzero");
else
bzero = NULL;
if(!use_shared_arrays) {
memory->create(uarraytot_r, jdim, jdim, jdim,
"sna:uarraytot");
@ -1541,6 +1555,9 @@ void SNA::destroy_twojmax_arrays()
memory->destroy(uarray_r);
memory->destroy(uarray_i);
if (bzero_flag)
memory->destroy(bzero);
if(!use_shared_arrays) {
memory->destroy(uarraytot_r);
memory->destroy(zarray_r);

4
src/SNAP/sna.h
View File

@ -31,7 +31,7 @@ struct SNA_LOOPINDICES {
class SNA : protected Pointers {
public:
SNA(LAMMPS*, double, int, int, int, double, int);
SNA(LAMMPS*, double, int, int, int, double, int, int);
SNA(LAMMPS* lmp) : Pointers(lmp) {};
~SNA();
@ -139,6 +139,8 @@ private:
// Self-weight
double wself;
int bzero_flag; // 1 if bzero subtracted from barray
double *bzero; // array of B values for isolated atoms
};
}

2
src/balance.cpp
View File

@ -256,6 +256,7 @@ void Balance::command(int narg, char **arg)
// insure particles are in current box & update box via shrink-wrap
// init entire system since comm->setup is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
// must reset atom map after exchange() since it clears it
MPI_Barrier(world);
double start_time = MPI_Wtime();
@ -267,6 +268,7 @@ void Balance::command(int narg, char **arg)
domain->reset_box();
comm->setup();
comm->exchange();
if (atom->map_style) atom->map_set();
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// imbinit = initial imbalance

3
src/comm.cpp
View File

@ -266,7 +266,8 @@ void Comm::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
if (mode == MULTI)
error->all(FLERR,"Use cutoff/multi keyword to set cutoff in multi mode");
error->all(FLERR,
"Use cutoff/multi keyword to set cutoff in multi mode");
cutghostuser = force->numeric(FLERR,arg[iarg+1]);
if (cutghostuser < 0.0)
error->all(FLERR,"Invalid cutoff in comm_modify command");

8
src/compute.cpp
View File

@ -127,11 +127,15 @@ void Compute::modify_params(int narg, char **arg)
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"extra") == 0) {
// added more specific keywords in Mar17
// at some point, remove generic extra and dynamic
if (strcmp(arg[iarg],"extra") == 0 ||
strcmp(arg[iarg],"extra/dof") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute_modify command");
extra_dof = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dynamic") == 0) {
} else if (strcmp(arg[iarg],"dynamic") == 0 ||
strcmp(arg[iarg],"dynamic/dof") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute_modify command");
if (strcmp(arg[iarg+1],"no") == 0) dynamic_user = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) dynamic_user = 1;

9
src/fix.cpp
View File

@ -71,6 +71,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) :
restart_pbc = 0;
wd_header = wd_section = 0;
dynamic_group_allow = 0;
dynamic = 0;
dof_flag = 0;
special_alter_flag = 0;
enforce2d_flag = 0;
@ -130,7 +131,13 @@ void Fix::modify_params(int narg, char **arg)
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"energy") == 0) {
if (strcmp(arg[iarg],"dynamic/dof") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[iarg+1],"no") == 0) dynamic = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) dynamic = 1;
else error->all(FLERR,"Illegal fix_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"energy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[iarg+1],"no") == 0) thermo_energy = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) thermo_energy = 1;

2
src/fix.h
View File

@ -217,6 +217,8 @@ class Fix : protected Pointers {
int copymode; // if set, do not deallocate during destruction
// required when classes are used as functors by Kokkos
int dynamic; // recount atoms for temperature computes
void ev_setup(int, int);
void ev_tally(int, int *, double, double, double *);
void v_setup(int);

1
src/fix_momentum.h
View File

@ -34,7 +34,6 @@ class FixMomentum : public Fix {
protected:
int linear,angular,rescale;
int xflag,yflag,zflag;
int dynamic;
double masstotal;
};

1
src/fix_nh.cpp
View File

@ -811,7 +811,6 @@ void FixNH::setup(int vflag)
(etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
boltz * t_target) / etap_mass[ich];
}
}
}

3
src/library.cpp
View File

@ -862,7 +862,8 @@ void lammps_scatter_atoms(void *ptr, char *name,
int i,j,m,offset;
void *vptr = lmp->atom->extract(name);
if(vptr == NULL) {
lmp->error->warning(FLERR,"lammps_scatter_atoms: unknown property name");
lmp->error->warning(FLERR,
"lammps_scatter_atoms: unknown property name");
return;
}

6
src/special.cpp
View File

@ -75,8 +75,8 @@ void Special::build()
const double * const special_lj = force->special_lj;
const double * const special_coul = force->special_coul;
fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n"
" Special bond factors lj: %-10g %-10g %-10g\n"
" Special bond factors coul: %-10g %-10g %-10g\n",
" special bond factors lj: %-10g %-10g %-10g\n"
" special bond factors coul: %-10g %-10g %-10g\n",
special_lj[1],special_lj[2],special_lj[3],
special_coul[1],special_coul[2],special_coul[3]);
}
@ -498,6 +498,7 @@ void Special::dedup()
// re-create map
atom->map_init(0);
atom->nghost = 0;
atom->map_set();
}
@ -649,6 +650,7 @@ void Special::combine()
// re-create map
atom->map_init(0);
atom->nghost = 0;
atom->map_set();
}