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Merge pull request #289 from akohlmey/collected-updates-and-bugfixes 

Collected updates and bugfixes
This commit is contained in:
sjplimp 2016-11-30 14:02:41 -07:00 committed by GitHub
parent beb5a30f67 7ddb6670c0
commit d14814ae2e
42 changed files with 154 additions and 50 deletions
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10
doc/src/Section_commands.txt
View File

@ -632,11 +632,11 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"rigid/npt (o)"_fix_rigid.html,
"rigid/nve (o)"_fix_rigid.html,
"rigid/nvt (o)"_fix_rigid.html,
<"rigid/small (o)"_fix_rigid.html,
"rigid/small/nph"_fix_rigid.html,
"rigid/small/npt"_fix_rigid.html,
"rigid/small/nve"_fix_rigid.html,
"rigid/small/nvt"_fix_rigid.html,
"rigid/small (o)"_fix_rigid.html,
"rigid/small/nph (o)"_fix_rigid.html,
"rigid/small/npt (o)"_fix_rigid.html,
"rigid/small/nve (o)"_fix_rigid.html,
"rigid/small/nvt (o)"_fix_rigid.html,
"setforce (k)"_fix_setforce.html,
"shake"_fix_shake.html,
"spring"_fix_spring.html,

2
doc/src/compute_cluster_atom.txt
View File

@ -37,7 +37,7 @@ The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of a
{clsuter/atom} style.
{cluster/atom} style.
NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise

2
doc/src/compute_smd_contact_radius.txt
View File

@ -27,7 +27,7 @@ contact radius is used only to prevent particles belonging to
different physical bodies from penetrating each other. It is used by
the contact pair styles, e.g., smd/hertz and smd/tri_surface.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
The value of the contact radius will be 0.0 for particles not in the

2
doc/src/compute_smd_damage.txt
View File

@ -24,7 +24,7 @@ compute 1 all smd/damage :pre
Define a computation that calculates the damage status of SPH particles
according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Output Info:]

2
doc/src/compute_smd_hourglass_error.txt
View File

@ -32,7 +32,7 @@ configuration. This compute is only really useful for debugging the
hourglass control mechanim which is part of the Total-Lagrangian SPH
pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
Mach Dynamics in LAMMPS.
[Output Info:]

2
doc/src/compute_smd_internal_energy.txt
View File

@ -24,7 +24,7 @@ compute 1 all smd/internal/energy :pre
Define a computation which outputs the per-particle enthalpy, i.e.,
the sum of potential energy and heat.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
Mach Dynamics in LAMMPS.
[Output Info:]

2
doc/src/compute_smd_plastic_strain.txt
View File

@ -25,7 +25,7 @@ Define a computation that outputs the equivalent plastic strain per
particle. This command is only meaningful if a material model with
plasticity is defined.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
Mach Dynamics in LAMMPS.
[Output Info:]

2
doc/src/compute_smd_plastic_strain_rate.txt
View File

@ -25,7 +25,7 @@ Define a computation that outputs the time rate of the equivalent
plastic strain. This command is only meaningful if a material model
with plasticity is defined.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
Mach Dynamics in LAMMPS.
[Output Info:]

2
doc/src/compute_smd_rho.txt
View File

@ -26,7 +26,7 @@ The mass density is the mass of a particle which is constant during
the course of a simulation, divided by its volume, which can change
due to mechanical deformation.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_tlsph_defgrad.txt
View File

@ -25,7 +25,7 @@ Define a computation that calculates the deformation gradient. It is
only meaningful for particles which interact according to the
Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_tlsph_dt.txt
View File

@ -30,7 +30,7 @@ time step. This calculation is performed automatically in the
relevant SPH pair styles and this compute only serves to make the
stable time increment accessible for output purposes.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_tlsph_num_neighs.txt
View File

@ -25,7 +25,7 @@ Define a computation that calculates the number of particles inside of
the smoothing kernel radius for particles interacting via the
Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_tlsph_shape.txt
View File

@ -26,7 +26,7 @@ associated with a particle as a rotated ellipsoid. It is only
meaningful for particles which interact according to the
Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_tlsph_strain.txt
View File

@ -24,7 +24,7 @@ compute 1 all smd/tlsph/strain :pre
Define a computation that calculates the Green-Lagrange strain tensor
for particles interacting via the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_tlsph_strain_rate.txt
View File

@ -24,7 +24,7 @@ compute 1 all smd/tlsph/strain/rate :pre
Define a computation that calculates the rate of the strain tensor for
particles interacting via the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_tlsph_stress.txt
View File

@ -24,7 +24,7 @@ compute 1 all smd/tlsph/stress :pre
Define a computation that outputs the Cauchy stress tensor for
particles interacting via the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_triangle_mesh_vertices.txt
View File

@ -25,7 +25,7 @@ Define a computation that returns the coordinates of the vertices
corresponding to the triangle-elements of a mesh created by the "fix
smd/wall_surface"_fix_smd_wall_surface.html.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_ulsph_num_neighs.txt
View File

@ -25,7 +25,7 @@ Define a computation that returns the number of neighbor particles
inside of the smoothing kernel radius for particles interacting via
the updated Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_ulsph_strain.txt
View File

@ -24,7 +24,7 @@ compute 1 all smd/ulsph/strain :pre
Define a computation that outputs the logarithmic strain tensor. for
particles interacting via the updated Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_ulsph_strain_rate.txt
View File

@ -25,7 +25,7 @@ Define a computation that outputs the rate of the logarithmic strain
tensor for particles interacting via the updated Lagrangian SPH pair
style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_ulsph_stress.txt
View File

@ -23,7 +23,7 @@ compute 1 all smd/ulsph/stress :pre
Define a computation that outputs the Cauchy stress tensor.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/compute_smd_vol.txt
View File

@ -24,7 +24,7 @@ compute 1 all smd/vol :pre
Define a computation that provides the per-particle volume and the sum
of the per-particle volumes of the group for which the fix is defined.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
[Output info:]

2
doc/src/fix_smd_adjust_dt.txt
View File

@ -36,7 +36,7 @@ stable maximum time step.
This fix inquires the minimum stable time increment across all particles contained in the group for which this
fix is defined. An additional safety factor {s_fact} is applied to the time increment.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]

2
doc/src/fix_smd_integrate_tlsph.txt
View File

@ -32,7 +32,7 @@ fix 1 all smd/integrate_tlsph limit_velocity 1000 :pre
The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
The {limit_velocity} keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.

2
doc/src/fix_smd_integrate_ulsph.txt
View File

@ -34,7 +34,7 @@ fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre
[Description:]
The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are

2
doc/src/fix_smd_move_triangulated_surface.txt
View File

@ -55,7 +55,7 @@ specified. This style also sets the velocity of each particle to (omega cross
Rperp) where omega is its angular velocity around the rotation axis and
Rperp is a perpendicular vector from the rotation axis to the particle.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]

2
doc/src/fix_smd_wall_surface.txt
View File

@ -37,7 +37,7 @@ It is possible to move the triangulated surface via the "smd/move_tri_surf"_fix_
Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
in the system. See the "funnel_flow" example in the USER-SMD examples directory.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]

2
doc/src/pair_smd_tlsph.txt
View File

@ -39,7 +39,7 @@ invocation of the {tlsph} for a solid body would consist of an equation of state
the pressure (the diagonal components of the stress tensor), and a material model to compute shear
stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.
Please see the "SMD user guide"_USER/smd/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
:line

2
doc/src/pair_smd_ulsph.txt
View File

@ -43,7 +43,7 @@ stresses (the off-diagonal components of the stress tensor).
Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.
Please see the "SMD user guide"_USER/smd/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
:line

81
examples/USER/misc/grem/README Normal file
View File

@ -0,0 +1,81 @@
Generalized Replica Exchange Method (gREM) examples
===================================================
Examples:
---------------------------------------------------
lj-single:
This example is the simplest case scenario utilizing the generalized
ensemble defined by fix_grem. It utilizes only 1 replica and requires
the LAMMPS executable to be run as usual:
mpirun -np 4 lmp_mpi -in in.gREM-npt
./lmp_serial -in in.gREM-nvt
While this does not obtain any information about Ts(H), it is most similar to
a microcanonical simulation and "single-replica gREM" can be useful for
studying non-equilibrium processes as well.
lj-6rep:
This example utilizes an external python script to handle swaps between
replicas. Included is run.sh, which requires the path to your LAMMPS
executable. The python script is fragile as it relies on parsing output files
from the LAMMPS run and moving LAMMPS data files between directories. Use
caution if modifying this example further. If complied with mpi, multiple
processors can be used as:
./run.sh $NUM_PROCS
a serial run is completed simply as
./run.sh 1
where the executable provided must be serial if "1" is provided as the number
of procs. While this external replica exchange module is quite slow and
inefficient, it allows for many replicas to be used on a single processor.
While here there are only 6 replicas, this example could be extended to >100
replicas while still using a serial compilation. This is also beneficial for
running on high performance nodes with few cores to complete a full-scale gREM
simulation with a large number of replicas.
A quick note on efficiency: frequent exchanges slow down this script
substantially because LAMMPS is restarted every exchange attempt. The script
works best for large systems with infrequent exchanges.
lj-temper:
This is an example using the internal replica exchange module. While fast
in comparison to the python version, it requires substantial resources
(at least 1 proc per replica). Instead of stopping LAMMPS every exchange
attempt, all replicas are run concurrently, and exchanges take place
internally. This requires use of LAMMPS partition mode, via the command
line using the -p flag. Input files require world type variables defining
the parameters of each replica. The included example with 4 replicas must
run on at least 4 procs, in that case LAMMPS could be initiated as:
mpirun -np 4 lmp_mpi -p 4x1 -in in.gREM-temper
spawning 4 partitions with 1 replica each. Multiple procs per replica could
be used. In the case of a 16 system with 4 replicas, the
following logic could be used:
mpirun -np 16 lmp_mpi -p 4x4 -in in.gREM-temper
Once started, a universe log file will be created as well as log files for
each replica. The universe (log.lammps) contains exchange information, while
the replicas (*/log.lammps.*) contains the thermo_output as usual. In this
example, in.gREM-temper moves the log files to their respective folders.
Closing Notes:
---------------------------------------------------
Of significant difference between lj-6rep and lj-temper is the format of data.
In lj-6rep, data is stored as 'replicas' meaning discontinuous trajectories, as
files are moved between directories labeled by the 'lambda' of the replica. In
lj-temper, data is stored as 'walkers' with continuous trajectories, but
discontinuous parameters. The later is significantly more efficient, but
requires post-processing to obtain per-replica information.
Any problems/questions should be directed to <dstelter@bu.edu>.

3
examples/USER/misc/grem/lj-6rep/double-re-short.py
View File

@ -51,7 +51,7 @@ for exchange in arange(starting_ex,max_exchange):
os.chdir(path+"/%s" % lambdas[l])
#os.system("cp restart_file restart_file%d" % exchange)
if (nproc > 1):
os.system("mpirun -np %d " + lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (nproc, lambdas[l], eta, H))
os.system("mpirun -np %d " % (nproc) + lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (lambdas[l], eta, H))
if (nproc == 1):
os.system(lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (lambdas[l], eta, H))
os.system("grep -v '[a-zA-Z]' output | awk '{if(NF==6 && NR>19)print $0}' | awk '{print $3}' >ent")
@ -60,7 +60,6 @@ for exchange in arange(starting_ex,max_exchange):
aver_enthalpy[l] = mean(ee[-1])
# os.system("mv dump.dcd dump%d.dcd" % exchange)
os.system("mv log.lammps log%d.lammps" % exchange)
# os.system("rm output")
os.system("mv final_restart_file final_restart_file%d" % exchange)
os.system("mv ent ent%d" % exchange)
os.system("bzip2 log%d.lammps ent%d" % (exchange,exchange))

2
src/REPLICA/temper.cpp
View File

@ -84,6 +84,8 @@ void Temper::command(int narg, char **arg)
my_set_temp = universe->iworld;
if (narg == 7) my_set_temp = force->inumeric(FLERR,arg[6]);
if ((my_set_temp < 0) || (my_set_temp >= universe->nworlds))
error->universe_one(FLERR,"Illegal temperature index");
// swap frequency must evenly divide total # of timesteps

2
src/USER-MISC/README
View File

@ -29,7 +29,7 @@ bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
compute pressure/grem, David Stelter, dstelter@bu.edu, 22 Nov 16
compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16
dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
dihedral_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
dihedral_style nharmonic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12

2
src/USER-MISC/compute_pressure_grem.cpp
View File

@ -54,7 +54,7 @@ void ComputePressureGrem::init()
// Initialize hook to gREM fix
int ifix = modify->find_fix(fix_grem);
if (ifix < 0)
error->all(FLERR,"Fix grem ID for compute pressure/grem does not exist");
error->all(FLERR,"Fix grem ID for compute PRESSURE/GREM does not exist");
int dim;
scale_grem = (double *)modify->fix[ifix]->extract("scale_grem",dim);

8
src/USER-MISC/compute_pressure_grem.h
View File

@ -13,7 +13,7 @@
#ifdef COMPUTE_CLASS
ComputeStyle(pressure/grem,ComputePressureGrem)
ComputeStyle(PRESSURE/GREM,ComputePressureGrem)
#else
@ -80,12 +80,12 @@ E: Must use 'kspace_modify pressure/scalar no' for tensor components with kspace
Otherwise MSM will compute only a scalar pressure. See the kspace_modify
command for details on this setting.
E: Fix grem ID for compute pressure/grem does not exist
E: Fix grem ID for compute PRESSURE/GREM does not exist
Compute pressure/grem was passed an invalid fix id
Compute PRESSURE/GREM was passed an invalid fix id
E: Cannot extract gREM scale factor from fix grem
The fix id passed to compute pressure/grem refers to an incompatible fix
The fix id passed to compute PRESSURE/GREM refers to an incompatible fix
*/

19
src/USER-MISC/dihedral_nharmonic.cpp
View File

@ -35,7 +35,9 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
DihedralNHarmonic::DihedralNHarmonic(LAMMPS *lmp) : Dihedral(lmp) {}
DihedralNHarmonic::DihedralNHarmonic(LAMMPS *lmp) : Dihedral(lmp) {
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -334,3 +336,18 @@ void DihedralNHarmonic::read_restart(FILE *fp)
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void DihedralNHarmonic::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ndihedraltypes; i++) {
fprintf(fp, "%d %d", i, nterms[i]);
for (int j = 0; j < nterms[i]; j++ )
fprintf(fp, " %g", a[i][j]);
fprintf(fp, "\n");
}
}

1
src/USER-MISC/dihedral_nharmonic.h
View File

@ -33,6 +33,7 @@ class DihedralNHarmonic : public Dihedral {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
protected:
int *nterms;

2
src/USER-MISC/fix_grem.cpp
View File

@ -97,7 +97,7 @@ FixGrem::FixGrem(LAMMPS *lmp, int narg, char **arg) :
newarg = new char*[5];
newarg[0] = id_press;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure/grem";
newarg[2] = (char *) "PRESSURE/GREM";
newarg[3] = id_temp;
newarg[4] = id;
modify->add_compute(5,newarg);

1
src/USER-MISC/pair_agni.cpp
View File

@ -85,6 +85,7 @@ PairAGNI::PairAGNI(LAMMPS *lmp) : Pair(lmp)
nparams = 0;
params = NULL;
map = NULL;
cutmax = 0.0;
}
/* ----------------------------------------------------------------------

14
src/USER-MISC/temper_grem.cpp
View File

@ -113,6 +113,8 @@ void TemperGrem::command(int narg, char **arg)
my_set_lambda = universe->iworld;
if (narg == 8) my_set_lambda = force->inumeric(FLERR,arg[7]);
if ((my_set_lambda < 0) || (my_set_lambda >= universe->nworlds))
error->universe_one(FLERR,"Illegal temperature index");
// swap frequency must evenly divide total # of timesteps
@ -271,12 +273,6 @@ void TemperGrem::command(int narg, char **arg)
partner = world2root[partner_world];
}
// compute weights
volume = domain->xprd * domain->yprd * domain->zprd;
enth = pe + (pressref * volume);
weight = log(set_lambda[my_set_lambda] + (eta*(enth + h0)));
weight_cross = log(set_lambda[partner_set_lambda] + (eta*(enth + h0)));
// swap with a partner, only root procs in each world participate
// hi proc sends PE to low proc
// lo proc make Boltzmann decision on whether to swap
@ -284,6 +280,12 @@ void TemperGrem::command(int narg, char **arg)
swap = 0;
if (partner != -1) {
// compute weights
volume = domain->xprd * domain->yprd * domain->zprd;
enth = pe + (pressref * volume);
weight = log(set_lambda[my_set_lambda] + (eta*(enth + h0)));
weight_cross = log(set_lambda[partner_set_lambda] + (eta*(enth + h0)));
if (me_universe > partner) {
MPI_Send(&weight,1,MPI_DOUBLE,partner,0,universe->uworld);
MPI_Send(&weight_cross,1,MPI_DOUBLE,partner,0,universe->uworld);

1
src/compute_rdf.cpp
View File

@ -46,6 +46,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
array_flag = 1;
extarray = 0;
dynamic_group_allow = 0;
nbin = force->inumeric(FLERR,arg[3]);
if (nbin < 1) error->all(FLERR,"Illegal compute rdf command");

2
tools/msi2lmp/frc_files/README
View File

@ -5,6 +5,6 @@ for use with msi2lmp.
Note that LAMMPS does not distribute Accelrys (or old BioSym)
force field files, since they are proprietary. All the
files in this directory that are part of the LAMMPS distribution
are are openly available files that are in the public domain.
are openly available files that are in the public domain.