ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #9 from lammps/master

Browse Source 
rebase
This commit is contained in:
Jacob Gissinger
2018-04-24 22:09:17 -06:00
committed by GitHub
parent 020fc66ad9 d5ec76290b
commit 69665c218a
244 changed files with 3317 additions and 1605 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
cmake/CMakeLists.txt
View File

@ -240,8 +240,8 @@ if(ENABLE_LATTE)
message(STATUS "LATTE not found - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
URL https://github.com/lanl/LATTE/archive/v1.0.1.tar.gz
URL_MD5 5137e28cb1a64444bd571c98c98a6eee
URL https://github.com/lanl/LATTE/archive/v1.1.1.tar.gz
URL_MD5 cb86f1d2473ce00aa61ff6a023154b03
SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
)
@ -290,7 +290,21 @@ if(ENABLE_USER-VTK)
endif()
if(ENABLE_KIM)
find_package(KIM REQUIRED)
find_package(KIM QUIET)
if(NOT KIM_FOUND)
message(STATUS "KIM not found - we will build our own")
include(ExternalProject)
ExternalProject_Add(kim_build
URL https://github.com/openkim/kim-api/archive/v1.9.4.tar.gz
URL_MD5 f4d35a1705eed46d64c7c0ab448ff3e0
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
)
ExternalProject_get_property(kim_build INSTALL_DIR)
set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
list(APPEND LAMMPS_DEPS kim_build)
endif()
list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
include_directories(${KIM_INCLUDE_DIRS})
endif()

31
doc/src/Developer/developer.tex
View File

@ -449,15 +449,15 @@ Writing fixes is a flexible way of extending LAMMPS. Users can
implement many things using fixes:
\begin{itemize}
\item changing particles attributes (positions, velocities, forces, etc.).
\item changing particles attributes (positions, velocities, forces, etc.).
Example: FixFreeze.
\item reading/writing data. Example: FixRestart.
\item implementing boundary conditions. Example: FixWall.
\item saving information about particles for future use (previous positions,
\item saving information about particles for future use (previous positions,
for instance). Example: FixStoreState.
\end{itemize}
All fixes are derived from class Fix and must have constructor with the
All fixes are derived from class Fix and must have constructor with the
signature: FixMine(class LAMMPS *, int, char **).
Every fix must be registered in LAMMPS by writing the following lines
@ -478,7 +478,7 @@ included in the file "style\_fix.h". In case if you use LAMMPS make,
this file is generated automatically - all files starting with prefix
fix\_ are included, so call your header the same way. Otherwise, don<6F>t
forget to add your include into "style\_fix.h".
Let's write a simple fix which will print average velocity at the end
of each timestep. First of all, implement a constructor:
@ -487,11 +487,11 @@ of each timestep. First of all, implement a constructor:
FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
: Fix(lmp, narg, arg)
{
if (narg < 4)
if (narg < 4)
error->all(FLERR,"Illegal fix print command");
nevery = atoi(arg[3]);
if (nevery <= 0)
if (nevery <= 0)
error->all(FLERR,"Illegal fix print command");
}
\end{verbatim}
@ -545,7 +545,7 @@ void FixPrintVel::end_of_step()
{
// for add3, scale3
using namespace MathExtra;
double** v = atom->v;
int nlocal = atom->nlocal;
double localAvgVel[4]; // 4th element for particles count
@ -559,7 +559,7 @@ void FixPrintVel::end_of_step()
MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
scale3(1.0 / globalAvgVel[3], globalAvgVel);
if (comm->me == 0) {
printf("\%e, \%e, \%e\n",
printf("\%e, \%e, \%e\n",
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
}
}
@ -607,14 +607,15 @@ this situation there are several methods which should be implemented:
\begin{itemize}
\item \verb|double memory_usage| - return how much memory fix uses
\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
in your fix
\item \verb|void copy_arrays(int i, int j)| - copy i-th per-particle information
to j-th. Used when atoms sorting is performed
\item \verb|void copy_arrays(int i, int j, int delflag)| - copy i-th per-particle
information to j-th. Used when atoms sorting is performed. if delflag is set
and atom j owns a body, move the body information to atom i.
\item \verb|void set_arrays(int i)| - sets i-th particle related information to zero
\end{itemize}
Note, that if your class implements these methods, it must call add calls of
Note, that if your class implements these methods, it must call add calls of
add\_callback and delete\_callback to constructor and destructor:
\begin{center}
@ -654,7 +655,7 @@ void FixSavePos::grow_arrays(int nmax)
memory->grow(this->x, nmax, 3, "FixSavePos:x");
}
void FixSavePos::copy_arrays(int i, int j)
void FixSavePos::copy_arrays(int i, int j, int delflag)
{
memcpy(this->x[j], this->x[i], sizeof(double) * 3);
}
@ -670,7 +671,7 @@ int FixSavePos::pack_exchange(int i, double *buf)
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
return m;
}

4
doc/src/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="30 Mar 2018 version">
<META NAME="docnumber" CONTENT="20 Apr 2018 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -19,7 +19,7 @@
:line
LAMMPS Documentation :c,h1
30 Mar 2018 version :c,h2
20 Apr 2018 version :c,h2
Version info: :h3

40
doc/src/Section_errors.txt
View File

@ -1565,15 +1565,6 @@ This operation is not allowed. :dd
This operation is not allowed. :dd
{Cannot use -cuda on and -kokkos on together} :dt
This is not allowed since both packages can use GPUs. :dd
{Cannot use -cuda on without USER-CUDA installed} :dt
The USER-CUDA package must be installed via "make yes-user-cuda"
before LAMMPS is built. :dd
{Cannot use -kokkos on without KOKKOS installed} :dt
Self-explanatory. :dd
@ -1597,11 +1588,6 @@ solver/pair style. :dd
This is a current restriction of this command. :dd
{Cannot use GPU package with USER-CUDA package enabled} :dt
You cannot use both the GPU and USER-CUDA packages
together. Use one or the other. :dd
{Cannot use Kokkos pair style with rRESPA inner/middle} :dt
Self-explanatory. :dd
@ -8252,12 +8238,6 @@ Self-explanatory. :dd
The package command cannot be used afer a read_data, read_restart, or
create_box command. :dd
{Package cuda command without USER-CUDA package enabled} :dt
The USER-CUDA package must be installed via "make yes-user-cuda"
before LAMMPS is built, and the "-c on" must be used to enable the
package. :dd
{Package gpu command without GPU package installed} :dt
The GPU package must be installed via "make yes-gpu" before LAMMPS is
@ -10230,22 +10210,6 @@ it in different ways. :dd
Self-explanatory. :dd
{USER-CUDA mode requires CUDA variant of min style} :dt
CUDA mode is enabled, so the min style must include a cuda suffix. :dd
{USER-CUDA mode requires CUDA variant of run style} :dt
CUDA mode is enabled, so the run style must include a cuda suffix. :dd
{USER-CUDA package does not yet support comm_style tiled} :dt
Self-explanatory. :dd
{USER-CUDA package requires a cuda enabled atom_style} :dt
Self-explanatory. :dd
{Unable to initialize accelerator for use} :dt
There was a problem initializing an accelerator for the gpu package :dd
@ -10494,10 +10458,6 @@ Must use remap v option with fix deform with this pair style. :dd
If fix deform is used, the remap v option is required. :dd
{Using suffix cuda without USER-CUDA package enabled} :dt
Self-explanatory. :dd
{Using suffix gpu without GPU package installed} :dt
Self-explanatory. :dd

6
doc/src/Section_intro.txt
View File

@ -526,14 +526,14 @@ and efforts.
Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages
Roy Pollock (LLNL), Ewald and PPPM solvers
Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC)
Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA (obsoleted by KOKKOS) and KOKKOS packages
Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork for granular models and granular/fluid coupling
Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul

16
doc/src/compute_heat_flux.txt
View File

@ -26,14 +26,16 @@ compute myFlux all heat/flux myKE myPE myStress :pre
Define a computation that calculates the heat flux vector based on
contributions from atoms in the specified group. This can be used by
itself to measure the heat flux into or out of a reservoir of atoms,
or to calculate a thermal conductivity using the Green-Kubo formalism.
itself to measure the heat flux through a set of atoms (e.g. a region
between two thermostatted reservoirs held at different temperatures),
or to calculate a thermal conductivity using the equilibrium
Green-Kubo formalism.
See the "fix thermal/conductivity"_fix_thermal_conductivity.html
command for details on how to compute thermal conductivity in an
alternate way, via the Muller-Plathe method. See the "fix
heat"_fix_heat.html command for a way to control the heat added or
subtracted to a group of atoms.
For other non-equilibrium ways to compute a thermal conductivity, see
"this section"_Section_howto.html#howto_20. These include use of the
"fix thermal/conductivity"_fix_thermal_conductivity.html command for
the Muller-Plathe method. Or the "fix heat"_fix_heat.html command
which can add or subtract heat from groups of atoms.
The compute takes three arguments which are IDs of other
"computes"_compute.html. One calculates per-atom kinetic energy

8
doc/src/write_data.txt
View File

@ -16,6 +16,7 @@ file = name of data file to write out :ulb,l
zero or more keyword/value pairs may be appended :l
keyword = {pair} or {nocoeff} :l
{nocoeff} = do not write out force field info
{nofix} = do not write out extra sections read by fixes
{pair} value = {ii} or {ij}
{ii} = write one line of pair coefficient info per atom type
{ij} = write one line of pair coefficient info per IJ atom type pair :pre
@ -83,6 +84,12 @@ be written to the data file. This can be very helpful, if one wants
to make significant changes to the force field or if the parameters
are read in separately anyway, e.g. from an include file.
The {nofix} keyword requests that no extra sections read by fixes
should be written to the data file (see the {fix} option of the
"read_data"_read_data.html command for details). For example, this
option excludes sections for user-created per-atom properties
from "fix property/atom"_fix_property_atom.html.
The {pair} keyword lets you specify in what format the pair
coefficient information is written into the data file. If the value
is specified as {ii}, then one line per atom type is written, to
@ -120,4 +127,3 @@ setup, atom masses initialized, etc).
[Default:]
The option defaults are pair = ii.

7
examples/gcmc/in.gcmc.co2
View File

@ -59,7 +59,9 @@ timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix_modify myrigidnvt dynamic/dof no
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
# gcmc
@ -82,7 +84,10 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
# dynamically update default temperature ndof
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000

17
examples/gcmc/in.gcmc.h2o
View File

@ -30,8 +30,6 @@ create_box 2 box &
extra/angle/per/atom 1 &
extra/special/per/atom 2
# we can load multiple molecule templates, but don't have to use them all
molecule co2mol CO2.txt
molecule h2omol H2O.txt
create_atoms 0 box mol h2omol 464563 units box
@ -58,18 +56,24 @@ timestep 1.0
minimize 0.0 0.0 100 1000
reset_timestep 0
# rigid constraints with thermostat
fix mynvt all nvt temp ${temp} ${temp} 100
fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
# gcmc
fix mynvt h2o nvt temp ${temp} ${temp} 100
fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
# important to make temperature dofs dynamic
compute_modify thermo_temp dynamic/dof yes
compute_modify mynvt_temp dynamic/dof yes
run 1000
reset_timestep 0
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
h2omol tfac_insert ${tfac} group h2o shake wshake
# atom counts
@ -87,7 +91,6 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000

192
examples/gcmc/log.23Oct17.gcmc.co2.g++.4
View File

@ -1,192 +0,0 @@
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00261331 secs
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
24 atoms in group co2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
8 rigid bodies with 24 atoms
1.16 = max distance from body owner to body atom
fix_modify myrigidnvt dynamic/dof no
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
dynamic group carbon defined
group oxygen dynamic all var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.164636
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.41 | 15.41 | 15.41 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10
2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6
3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26
4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28
5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0 14 28
6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0 15 30
7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0 15 30
8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0 13 26
9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0 15 30
10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0 14 28
11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0 15 30
12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0 15 30
13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0 15 30
14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0 14 28
15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0 14 28
16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0 14 28
17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0 14 28
18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0 15 30
19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0 15 30
20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0 15 30
Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms
Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1687 | 1.6702 | 2.1864 | 30.8 | 5.15
Bond | 0.018828 | 0.020035 | 0.020975 | 0.6 | 0.06
Kspace | 0.57506 | 1.0931 | 1.5898 | 37.7 | 3.37
Neigh | 0.068863 | 0.069524 | 0.070128 | 0.2 | 0.21
Comm | 2.0735 | 2.0865 | 2.0979 | 0.7 | 6.43
Output | 0.0025017 | 0.0025966 | 0.0027781 | 0.2 | 0.01
Modify | 27.335 | 27.344 | 27.363 | 0.2 | 84.27
Other | | 0.1621 | | | 0.50
Nlocal: 11.25 ave 14 max 8 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 2639.75 ave 2656 max 2617 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 4320 ave 5824 max 2201 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 17280
Ave neighs/atom = 384
Ave special neighs/atom = 2
Neighbor list builds = 20394
Dangerous builds = 0
Total wall time: 0:00:32

293
examples/gcmc/log.23Oct17.gcmc.h2o.g++.4
View File

@ -1,293 +0,0 @@
LAMMPS (23 Oct 2017)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
# we can load multiple molecule templates, but don't have to use them all
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
molecule h2omol H2O.txt
Read molecule h2omol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00174451 secs
# rigid SPC/E water model
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_coeff 1 1000 1.0
angle_coeff 1 100 109.47
# masses
mass 1 15.9994
mass 2 1.0
# MD settings
group h2o type 1 2
24 atoms in group h2o
neighbor 2.0 bin
neigh_modify every 1 delay 1 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
minimize 0.0 0.0 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
Step Temp E_pair E_mol TotEng Press
0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
100 338 -15.742442 0.14954269 7.579918 -637.49568
Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-4.96106135393 -15.5388622715 -15.592899346
Force two-norm initial, final = 15.474 18.1478
Force max component initial, final = 5.80042 7.56514
Final line search alpha, max atom move = 0.00151131 0.0114333
Iterations, force evaluations = 100 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0085177 | 0.016083 | 0.026787 | 5.3 | 28.41
Bond | 0.00022459 | 0.00031394 | 0.00037575 | 0.0 | 0.55
Kspace | 0.0049062 | 0.014122 | 0.02044 | 5.0 | 24.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.018515 | 0.02086 | 0.023246 | 1.2 | 36.84
Output | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 | 0.0 | 0.05
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005213 | | | 9.21
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 1722 ave 1725 max 1720 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 1256.75 ave 2101 max 667 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 5027
Ave neighs/atom = 209.458
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# rigid constraints with thermostat
fix mynvt all nvt temp ${temp} ${temp} 100
fix mynvt all nvt temp 338.0 ${temp} 100
fix mynvt all nvt temp 338.0 338.0 100
fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
8 = # of frozen angles
# gcmc
run 1000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -15.742442 0 7.4303753 -613.0781
1000 369.81793 -54.202686 0 -37.667331 294.98823
Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms
Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0154 | 0.028993 | 0.040525 | 5.5 | 18.72
Bond | 0.00016999 | 0.0001902 | 0.00023293 | 0.0 | 0.12
Kspace | 0.019093 | 0.028112 | 0.038976 | 4.3 | 18.15
Neigh | 0.0020263 | 0.0022184 | 0.002408 | 0.4 | 1.43
Comm | 0.04947 | 0.053627 | 0.058009 | 1.4 | 34.62
Output | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 | 0.0 | 0.02
Modify | 0.035275 | 0.036815 | 0.038425 | 0.7 | 23.77
Other | | 0.004909 | | | 3.17
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 1331.5 ave 1369 max 1290 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 1259.75 ave 1642 max 428 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 5039
Ave neighs/atom = 209.958
Ave special neighs/atom = 2
Neighbor list builds = 27
Dangerous builds = 0
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# atom counts
variable oxygen atom "type==1"
variable hydrogen atom "type==2"
group oxygen dynamic all var oxygen
dynamic group oxygen defined
group hydrogen dynamic all var hydrogen
dynamic group hydrogen defined
variable nO equal count(oxygen)
variable nH equal count(hydrogen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0 8 16
2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0 29 58
3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0 33 66
4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0 33 66
5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0 33 66
6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0 33 66
7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0 33 66
8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0 33 66
9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0 34 68
10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0 34 68
11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0 34 68
12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0 34 68
13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0 34 68
14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0 34 68
15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0 34 68
16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0 34 68
17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0 34 68
18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0 34 68
19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0 35 70
20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0 35 70
21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0 35 70
Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms
Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.3571 | 9.7574 | 13.984 | 90.7 | 11.56
Bond | 0.026374 | 0.031321 | 0.035482 | 2.1 | 0.04
Kspace | 0.57402 | 4.7894 | 8.1754 | 129.0 | 5.67
Neigh | 0.34952 | 0.34987 | 0.35021 | 0.1 | 0.41
Comm | 2.4028 | 2.4228 | 2.4372 | 0.9 | 2.87
Output | 0.0012269 | 0.0012826 | 0.0014355 | 0.2 | 0.00
Modify | 66.819 | 66.828 | 66.837 | 0.1 | 79.17
Other | | 0.2281 | | | 0.27
Nlocal: 26.25 ave 31 max 22 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 6049.25 ave 6133 max 5962 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 23613 ave 35083 max 14025 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 94452
Ave neighs/atom = 899.543
Ave special neighs/atom = 2
Neighbor list builds = 20428
Dangerous builds = 0
Total wall time: 0:01:24

120
examples/gcmc/log.23Oct17.gcmc.co2.g++.1 → examples/gcmc/log.30Mar18.gcmc.co2.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (23 Oct 2017)
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
@ -39,14 +39,14 @@ Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00196958 secs
Time spent = 0.00241756 secs
# rigid CO2 TraPPE model
@ -72,29 +72,31 @@ timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
8 rigid bodies with 24 atoms
1.16 = max distance from body owner to body atom
fix_modify myrigidnvt dynamic/dof no
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic all var carbon
group carbon dynamic co2 var carbon
dynamic group carbon defined
group oxygen dynamic all var oxygen
group oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
@ -105,7 +107,10 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
# dynamically update default temperature ndof
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
@ -113,13 +118,13 @@ thermo 1000
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.164636
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
@ -138,55 +143,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16
2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20
3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14
4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0 9 18
5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0 9 18
6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0 10 20
7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0 12 24
8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0 8 16
9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0 1 2
10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0 13 26
11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0 11 22
12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0 0 0
13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0 2 4
14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0 5 10
15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0 9 18
16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0 12 24
17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0 10 20
18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0 3 6
19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0 8 16
20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0 10 20
Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms
1000 330.05964 -376.0111 -13.936335 13.773831 0.65771539 27 0.21142067 0.21453147 0 0 9 18
2000 293.79769 -321.3209 -19.049256 13.720163 0.73079488 30 0.25170944 0.25426294 0 0 10 20
3000 348.9085 259.04079 -0.23347965 2.4267366 0.14615898 6 0.22016906 0.23200597 0 0 2 4
4000 360.54577 -329.12072 -16.584234 15.046059 0.65771539 27 0.19173099 0.19785362 0 0 9 18
5000 275.58628 -58.283006 -12.520856 11.500585 0.65771539 27 0.16490585 0.17329884 0 0 9 18
6000 338.59574 364.93514 -19.866569 17.494353 0.80387436 33 0.17971759 0.18331589 0 0 11 22
7000 286.11586 -1252.5069 -19.588667 13.361427 0.73079488 30 0.15729895 0.16220459 0 0 10 20
8000 454.86786 -642.89382 -20.818357 21.242037 0.73079488 30 0.15500235 0.15802382 0 0 10 20
9000 326.36695 -364.71382 -31.376162 18.48392 0.87695385 36 0.14203985 0.14510714 0 0 12 24
10000 348.46961 -387.75245 -21.068466 18.00451 0.80387436 33 0.14000907 0.14343389 0 0 11 22
11000 409.74257 -15.843895 -20.648252 21.170323 0.80387436 33 0.14689306 0.15117074 0 0 11 22
12000 523.93502 1003.0729 -6.0563102 14.055757 0.43847693 18 0.15337575 0.1580166 0 0 6 12
13000 278.14441 -717.1097 -2.3488496 4.6982087 0.29231795 12 0.15952356 0.16422306 0 0 4 8
14000 367.89375 1239.0841 -11.203323 13.524997 0.5846359 24 0.17002439 0.17460294 0 0 8 16
15000 197.05319 -471.14343 -9.3890758 6.2653668 0.51155641 21 0.17702612 0.18155802 0 0 7 14
16000 138.17147 -935.93437 -2.3846783 2.3338898 0.29231795 12 0.17884346 0.18268758 0 0 4 8
17000 245.61833 -166.1694 -5.0970057 5.3690384 0.36539744 15 0.18909252 0.19317817 0 0 5 10
18000 232.0142 -175.732 -14.320198 9.6822635 0.65771539 27 0.18977089 0.19280537 0 0 9 18
19000 362.01189 864.87258 -6.4515321 9.7117982 0.43847693 18 0.19207244 0.19488984 0 0 6 12
20000 441.19548 186.19779 -18.147268 20.603546 0.73079488 30 0.19713351 0.199073 0 0 10 20
Loop time of 16.4949 on 1 procs for 20000 steps with 30 atoms
Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 104.760 ns/day, 0.229 hours/ns, 1212.498 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5462 | 2.5462 | 2.5462 | 0.0 | 12.30
Bond | 0.029783 | 0.029783 | 0.029783 | 0.0 | 0.14
Kspace | 0.26167 | 0.26167 | 0.26167 | 0.0 | 1.26
Neigh | 0.10705 | 0.10705 | 0.10705 | 0.0 | 0.52
Comm | 0.23409 | 0.23409 | 0.23409 | 0.0 | 1.13
Output | 0.0013416 | 0.0013416 | 0.0013416 | 0.0 | 0.01
Modify | 17.458 | 17.458 | 17.458 | 0.0 | 84.37
Other | | 0.05433 | | | 0.26
Pair | 1.8955 | 1.8955 | 1.8955 | 0.0 | 11.49
Bond | 0.026564 | 0.026564 | 0.026564 | 0.0 | 0.16
Kspace | 0.21215 | 0.21215 | 0.21215 | 0.0 | 1.29
Neigh | 0.088336 | 0.088336 | 0.088336 | 0.0 | 0.54
Comm | 0.19828 | 0.19828 | 0.19828 | 0.0 | 1.20
Output | 0.001025 | 0.001025 | 0.001025 | 0.0 | 0.01
Modify | 14.024 | 14.024 | 14.024 | 0.0 | 85.02
Other | | 0.0491 | | | 0.30
Nlocal: 30 ave 30 max 30 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2310 ave 2310 max 2310 min
Nghost: 2094 ave 2094 max 2094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7736 ave 7736 max 7736 min
Neighs: 7664 ave 7664 max 7664 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7736
Ave neighs/atom = 257.867
Total # of neighbors = 7664
Ave neighs/atom = 255.467
Ave special neighs/atom = 2
Neighbor list builds = 20349
Neighbor list builds = 20076
Dangerous builds = 0
Total wall time: 0:00:20
Total wall time: 0:00:16

131
examples/gcmc/log.30Mar18.gcmc.co2.g++.4 Normal file
View File

@ -0,0 +1,131 @@
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00257635 secs
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
24 atoms in group co2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
8 rigid bodies with 24 atoms
1.16 = max distance from body owner to body atom
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic co2 var carbon
dynamic group carbon defined
group oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
# dynamically update default temperature ndof
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
run 20000
Ewald initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.164636
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
Last command: run 20000

175
examples/gcmc/log.23Oct17.gcmc.h2o.g++.1 → examples/gcmc/log.30Mar18.gcmc.h2o.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (23 Oct 2017)
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
@ -34,24 +34,16 @@ create_box 2 box bond/types 1
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
# we can load multiple molecule templates, but don't have to use them all
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
molecule h2omol H2O.txt
Read molecule h2omol:
3 atoms with 2 types
2 bonds with 1 types
1 angles with 1 types
0 dihedrals with 0 types
0 impropers with 0 types
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00201297 secs
Time spent = 0.00204968 secs
# rigid SPC/E water model
@ -79,7 +71,7 @@ timestep 1.0
minimize 0.0 0.0 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
@ -101,9 +93,9 @@ Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
Step Temp E_pair E_mol TotEng Press
0 338 -4.1890564 9.2628112e-06 18.98377 739.06991
100 338 -30.182886 0.85607237 -6.1539961 -2535.3207
Loop time of 0.0507543 on 1 procs for 100 steps with 24 atoms
Loop time of 0.0512006 on 1 procs for 100 steps with 24 atoms
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
@ -117,14 +109,14 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.042597 | 0.042597 | 0.042597 | 0.0 | 83.93
Bond | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.94
Kspace | 0.0031135 | 0.0031135 | 0.0031135 | 0.0 | 6.13
Pair | 0.04303 | 0.04303 | 0.04303 | 0.0 | 84.04
Bond | 0.00047088 | 0.00047088 | 0.00047088 | 0.0 | 0.92
Kspace | 0.0029728 | 0.0029728 | 0.0029728 | 0.0 | 5.81
Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90
Comm | 0.0032997 | 0.0032997 | 0.0032997 | 0.0 | 6.50
Output | 1.359e-05 | 1.359e-05 | 1.359e-05 | 0.0 | 0.03
Comm | 0.003406 | 0.003406 | 0.003406 | 0.0 | 6.65
Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.04
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0007946 | | | 1.57
Other | | 0.0008392 | | | 1.64
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -139,23 +131,26 @@ Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
reset_timestep 0
# rigid constraints with thermostat
fix mynvt all nvt temp ${temp} ${temp} 100
fix mynvt all nvt temp 338.0 ${temp} 100
fix mynvt all nvt temp 338.0 338.0 100
fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
fix mynvt h2o nvt temp ${temp} ${temp} 100
fix mynvt h2o nvt temp 338.0 ${temp} 100
fix mynvt h2o nvt temp 338.0 338.0 100
fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
8 = # of frozen angles
# gcmc
# important to make temperature dofs dynamic
compute_modify thermo_temp dynamic/dof yes
compute_modify mynvt_temp dynamic/dof yes
run 1000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
@ -164,23 +159,23 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -30.182886 0 -7.0100684 993.1985
1000 326.9865 -62.258445 0 -47.638175 -5.3440813
Loop time of 0.141449 on 1 procs for 1000 steps with 24 atoms
1000 326.9865 -62.258443 0 -47.638173 -5.3439918
Loop time of 0.139436 on 1 procs for 1000 steps with 24 atoms
Performance: 610.819 ns/day, 0.039 hours/ns, 7069.663 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 619.641 ns/day, 0.039 hours/ns, 7171.773 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10788 | 0.10788 | 0.10788 | 0.0 | 76.27
Bond | 0.00018954 | 0.00018954 | 0.00018954 | 0.0 | 0.13
Kspace | 0.011867 | 0.011867 | 0.011867 | 0.0 | 8.39
Neigh | 0.0045254 | 0.0045254 | 0.0045254 | 0.0 | 3.20
Comm | 0.011277 | 0.011277 | 0.011277 | 0.0 | 7.97
Output | 1.5497e-05 | 1.5497e-05 | 1.5497e-05 | 0.0 | 0.01
Modify | 0.00383 | 0.00383 | 0.00383 | 0.0 | 2.71
Other | | 0.001868 | | | 1.32
Pair | 0.10588 | 0.10588 | 0.10588 | 0.0 | 75.94
Bond | 0.00015759 | 0.00015759 | 0.00015759 | 0.0 | 0.11
Kspace | 0.011144 | 0.011144 | 0.011144 | 0.0 | 7.99
Neigh | 0.00459 | 0.00459 | 0.00459 | 0.0 | 3.29
Comm | 0.011396 | 0.011396 | 0.011396 | 0.0 | 8.17
Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.01
Modify | 0.0043328 | 0.0043328 | 0.0043328 | 0.0 | 3.11
Other | | 0.001914 | | | 1.37
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -194,13 +189,16 @@ Ave neighs/atom = 213
Ave special neighs/atom = 2
Neighbor list builds = 25
Dangerous builds = 0
reset_timestep 0
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# atom counts
@ -219,7 +217,6 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
@ -227,67 +224,67 @@ thermo 1000
run 20000
Ewald initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0 8 16
2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0 25 50
3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0 30 60
4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0 33 66
5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0 34 68
6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0 34 68
7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0 34 68
8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0 34 68
9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0 34 68
10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0 34 68
11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0 34 68
12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0 34 68
13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0 34 68
14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0 34 68
15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0 35 70
16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0 35 70
17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0 35 70
18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0 35 70
19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0 35 70
20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0 36 72
21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0 36 72
Loop time of 220.662 on 1 procs for 20000 steps with 108 atoms
0 326.9865 -4.3508819 -62.258443 14.62027 0.23910963 24 0 0 0 0 8 16
1000 354.423 -3760.1354 -235.34169 51.766914 0.74721761 75 0.046175467 0.011949811 0 0 25 50
2000 335.19661 -3018.659 -270.44089 52.955344 0.80699501 81 0.026473882 0.0068755525 0 0 27 54
3000 333.47175 2657.2052 -336.48359 64.611037 0.98632724 99 0.022634978 0.0060076096 0 0 33 66
4000 321.48504 2055.4786 -345.06113 62.288579 0.98632724 99 0.016897769 0.0045269353 0 0 33 66
5000 333.45735 1918.5375 -368.5463 66.596193 1.0162159 102 0.013784412 0.0036569014 0 0 34 68
6000 301.90666 -698.74074 -371.32122 60.295069 1.0162159 102 0.01160439 0.0030159847 0 0 34 68
7000 336.42505 1537.9483 -378.51731 69.194524 1.0461046 105 0.010174953 0.0025995783 0 0 35 70
8000 338.95331 -1032.1084 -390.7067 69.714524 1.0461046 105 0.0089594585 0.002260114 0 0 35 70
9000 311.44605 -1494.7788 -383.9272 64.056945 1.0461046 105 0.007938083 0.0020156323 0 0 35 70
10000 330.70877 2082.4597 -366.57249 68.018822 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70
11000 286.34718 2238.3752 -370.91119 60.601806 1.0759934 108 0.0066641451 0.0016519521 0 0 36 72
12000 371.02522 3048.7157 -398.51333 78.522854 1.0759934 108 0.0061145907 0.0015128339 0 0 36 72
13000 392.87611 4486.1134 -387.07077 83.147323 1.0759934 108 0.0056427384 0.0013968431 0 0 36 72
14000 332.80747 3586.2698 -406.12151 70.434545 1.0759934 108 0.0052496417 0.0012945729 0 0 36 72
15000 325.61844 4198.3864 -387.5733 68.913077 1.0759934 108 0.0048934679 0.0012098238 0 0 36 72
16000 254.10285 1560.976 -409.98615 55.292559 1.1058821 111 0.0047204383 0.0011320612 0 0 37 74
17000 367.46414 2750.8283 -412.22037 79.959878 1.1058821 111 0.0044407568 0.0010659592 0 0 37 74
18000 407.74215 2308.5027 -408.73046 88.724338 1.1058821 111 0.0042016342 0.0010049017 0 0 37 74
19000 341.53799 5777.9814 -407.00637 74.31837 1.1058821 111 0.0039877848 0.00095025921 0 0 37 74
20000 395.75303 3159.4677 -403.82798 86.115516 1.1058821 111 0.0037874635 0.00090297077 0 0 37 74
Loop time of 231.351 on 1 procs for 20000 steps with 111 atoms
Performance: 7.831 ns/day, 3.065 hours/ns, 90.637 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 7.469 ns/day, 3.213 hours/ns, 86.449 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 37.459 | 37.459 | 37.459 | 0.0 | 16.98
Bond | 0.087067 | 0.087067 | 0.087067 | 0.0 | 0.04
Kspace | 0.90234 | 0.90234 | 0.90234 | 0.0 | 0.41
Neigh | 1.2299 | 1.2299 | 1.2299 | 0.0 | 0.56
Comm | 0.95437 | 0.95437 | 0.95437 | 0.0 | 0.43
Output | 0.0010636 | 0.0010636 | 0.0010636 | 0.0 | 0.00
Modify | 179.85 | 179.85 | 179.85 | 0.0 | 81.51
Other | | 0.1754 | | | 0.08
Pair | 39.09 | 39.09 | 39.09 | 0.0 | 16.90
Bond | 0.092728 | 0.092728 | 0.092728 | 0.0 | 0.04
Kspace | 0.87751 | 0.87751 | 0.87751 | 0.0 | 0.38
Neigh | 3.9658 | 3.9658 | 3.9658 | 0.0 | 1.71
Comm | 1.0608 | 1.0608 | 1.0608 | 0.0 | 0.46
Output | 0.00096035 | 0.00096035 | 0.00096035 | 0.0 | 0.00
Modify | 186.07 | 186.07 | 186.07 | 0.0 | 80.43
Other | | 0.1892 | | | 0.08
Nlocal: 108 ave 108 max 108 min
Nlocal: 111 ave 111 max 111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7850 ave 7850 max 7850 min
Nghost: 8070 ave 8070 max 8070 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99828 ave 99828 max 99828 min
Neighs: 105469 ave 105469 max 105469 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 99828
Ave neighs/atom = 924.333
Total # of neighbors = 105469
Ave neighs/atom = 950.171
Ave special neighs/atom = 2
Neighbor list builds = 20439
Neighbor list builds = 20910
Dangerous builds = 0
Total wall time: 0:03:40
Total wall time: 0:03:51

237
examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 Normal file
View File

@ -0,0 +1,237 @@
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
molecule h2omol H2O.txt
Read molecule h2omol:
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
Time spent = 0.00285625 secs
# rigid SPC/E water model
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_coeff 1 1000 1.0
angle_coeff 1 100 109.47
# masses
mass 1 15.9994
mass 2 1.0
# MD settings
group h2o type 1 2
24 atoms in group h2o
neighbor 2.0 bin
neigh_modify every 1 delay 1 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
minimize 0.0 0.0 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Ewald initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
Step Temp E_pair E_mol TotEng Press
0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
100 338 -15.742442 0.14954269 7.579918 -637.49568
Loop time of 0.0695416 on 4 procs for 100 steps with 24 atoms
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-4.96106135393 -15.5388622715 -15.592899346
Force two-norm initial, final = 15.474 18.1478
Force max component initial, final = 5.80042 7.56514
Final line search alpha, max atom move = 0.00151131 0.0114333
Iterations, force evaluations = 100 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0093951 | 0.017625 | 0.028943 | 5.3 | 25.34
Bond | 0.00035357 | 0.00042325 | 0.00055075 | 0.0 | 0.61
Kspace | 0.00664 | 0.019695 | 0.029924 | 6.1 | 28.32
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.022505 | 0.02509 | 0.027851 | 1.3 | 36.08
Output | 3.3855e-05 | 3.5942e-05 | 4.1485e-05 | 0.0 | 0.05
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006672 | | | 9.59
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 1722 ave 1725 max 1720 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 1256.75 ave 2101 max 667 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 5027
Ave neighs/atom = 209.458
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
# rigid constraints with thermostat
fix mynvt h2o nvt temp ${temp} ${temp} 100
fix mynvt h2o nvt temp 338.0 ${temp} 100
fix mynvt h2o nvt temp 338.0 338.0 100
fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
8 = # of frozen angles
# important to make temperature dofs dynamic
compute_modify thermo_temp dynamic/dof yes
compute_modify mynvt_temp dynamic/dof yes
run 1000
Ewald initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -15.742442 0 7.4303753 -613.0781
1000 369.81793 -54.202682 0 -37.667327 294.98832
Loop time of 0.191619 on 4 procs for 1000 steps with 24 atoms
Performance: 450.894 ns/day, 0.053 hours/ns, 5218.680 timesteps/s
96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.015873 | 0.028989 | 0.040172 | 5.3 | 15.13
Bond | 0.00024271 | 0.00027657 | 0.00034404 | 0.0 | 0.14
Kspace | 0.022896 | 0.034492 | 0.047924 | 5.1 | 18.00
Neigh | 0.0025764 | 0.0025961 | 0.0026152 | 0.0 | 1.35
Comm | 0.068467 | 0.070095 | 0.071535 | 0.4 | 36.58
Output | 4.8161e-05 | 5.0783e-05 | 5.7936e-05 | 0.0 | 0.03
Modify | 0.049141 | 0.049894 | 0.05072 | 0.3 | 26.04
Other | | 0.005226 | | | 2.73
Nlocal: 6 ave 8 max 3 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 1331.5 ave 1369 max 1290 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 1259.75 ave 1642 max 428 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 5039
Ave neighs/atom = 209.958
Ave special neighs/atom = 2
Neighbor list builds = 27
Dangerous builds = 0
reset_timestep 0
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# atom counts
variable oxygen atom "type==1"
variable hydrogen atom "type==2"
group oxygen dynamic all var oxygen
dynamic group oxygen defined
group hydrogen dynamic all var hydrogen
dynamic group hydrogen defined
variable nO equal count(oxygen)
variable nH equal count(hydrogen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo 1000
# run
run 20000
Ewald initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
Last command: run 20000

67
examples/gcmc/log.23Oct17.gcmc.lj.g++.1 → examples/gcmc/log.30Mar18.gcmc.lj.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (23 Oct 2017)
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5)
pair_coeff * * 1.0 1.0
mass * 1.0
# we recommend setting up a dedicated group for gcmc
group gcmcgroup type 1
0 atoms in group gcmcgroup
# gcmc
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
group type1 dynamic gcmcgroup var type1
dynamic group type1 defined
variable n1 equal count(type1)
@ -97,40 +102,40 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219 64.98
2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004 62.97
3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537 63.5
4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657 62.17
5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777 64.15
6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359 64.37
7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399 62.33
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766 64.29
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544 62.87
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094 63.2
Loop time of 20.4081 on 1 procs for 10000 steps with 60 atoms
1000 2.0603874 2.9024736 -3.2576986 3.0482443 0.584 73 0.069266074 0.066959582 0.11158434 0.53624 1.3978532 0.0014407586 64.19
2000 2.1586837 1.5581387 -2.8420766 3.1857993 0.496 62 0.068487803 0.067570935 0.1126652 0.53128 1.3713694 0.020274019 63.41
3000 2.4664064 0.65471138 -3.3428236 3.6435549 0.528 66 0.068182273 0.067547792 0.11226502 0.53472 1.3892234 0.0070204504 63.68
4000 1.8880496 1.4802782 -2.7846019 2.785647 0.488 61 0.068250075 0.067843541 0.11299989 0.52744 1.299496 0.033918563 63.1
5000 2.0578649 1.3204331 -3.5571862 3.0433213 0.568 71 0.067858571 0.067732262 0.11271981 0.5364 1.4237505 0.00065741209 64
6000 2.3627973 0.97064566 -3.1107668 3.4879388 0.504 63 0.067846204 0.06757018 0.11272207 0.5332 1.3945131 0.014216594 63.7
7000 1.6629817 0.98138972 -2.7780297 2.4514644 0.464 58 0.067451389 0.067269791 0.11263692 0.53688 1.4207486 -0.0012887793 63.82
8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 62.43
9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 63.23
10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 62.44
Loop time of 21.2409 on 1 procs for 10000 steps with 64 atoms
Performance: 211680.375 tau/day, 490.001 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 203381.368 tau/day, 470.790 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.46484 | 0.46484 | 0.46484 | 0.0 | 2.28
Neigh | 1.1447 | 1.1447 | 1.1447 | 0.0 | 5.61
Comm | 0.1696 | 0.1696 | 0.1696 | 0.0 | 0.83
Output | 0.000319 | 0.000319 | 0.000319 | 0.0 | 0.00
Modify | 18.607 | 18.607 | 18.607 | 0.0 | 91.17
Other | | 0.02194 | | | 0.11
Pair | 0.45931 | 0.45931 | 0.45931 | 0.0 | 2.16
Neigh | 1.1637 | 1.1637 | 1.1637 | 0.0 | 5.48
Comm | 0.17294 | 0.17294 | 0.17294 | 0.0 | 0.81
Output | 0.00027394 | 0.00027394 | 0.00027394 | 0.0 | 0.00
Modify | 19.416 | 19.416 | 19.416 | 0.0 | 91.41
Other | | 0.02919 | | | 0.14
Nlocal: 60 ave 60 max 60 min
Nlocal: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 663 ave 663 max 663 min
Nghost: 714 ave 714 max 714 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2133 ave 2133 max 2133 min
Neighs: 2423 ave 2423 max 2423 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2133
Ave neighs/atom = 35.55
Total # of neighbors = 2423
Ave neighs/atom = 37.8594
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:20
Total wall time: 0:00:21

73
examples/gcmc/log.23Oct17.gcmc.lj.g++.4 → examples/gcmc/log.30Mar18.gcmc.lj.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (23 Oct 2017)
LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5)
pair_coeff * * 1.0 1.0
mass * 1.0
# we recommend setting up a dedicated group for gcmc
group gcmcgroup type 1
0 atoms in group gcmcgroup
# gcmc
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
group type1 dynamic all var type1
group type1 dynamic gcmcgroup var type1
dynamic group type1 defined
variable n1 equal count(type1)
@ -97,40 +102,40 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866 63.44
2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794 62.19
3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578 63.23
4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078 62.57
5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867 62.56
6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549 63.76
7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793 62.2
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191 62.03
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837 64.36
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238 63.24
Loop time of 23.8213 on 4 procs for 10000 steps with 69 atoms
1000 2.4378552 1.9014939 -3.23439 3.6030066 0.544 68 0.073050445 0.070796636 0.11934255 0.52552 1.3006333 0.04152087 62.56
2000 1.9339159 1.0360287 -3.5001391 2.8594327 0.56 70 0.069588893 0.068587488 0.11319584 0.542 1.4012888 -0.020696665 64.56
3000 1.8891807 2.2857708 -3.3755633 2.7954769 0.592 74 0.068329031 0.067640916 0.11187803 0.53536 1.3380926 0.0062359288 64.21
4000 2.0436517 1.7600211 -3.4067452 3.0229014 0.576 72 0.067464211 0.067003868 0.11060324 0.54144 1.4484907 -0.016246603 64.75
5000 2.1512268 1.0811095 -3.2418366 3.1786785 0.536 67 0.066830654 0.066717982 0.1094094 0.54368 1.4962073 -0.025791643 65.04
6000 2.128931 1.5444487 -3.1904474 3.1450116 0.528 66 0.067479197 0.067193531 0.1104464 0.53112 1.4247377 0.019908014 63.01
7000 1.8194311 0.72981963 -3.6601329 2.6912418 0.576 72 0.068131849 0.067910074 0.11182024 0.51968 1.4517098 0.063444774 61.72
8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45
9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73
10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04
Loop time of 29.2417 on 4 procs for 10000 steps with 60 atoms
Performance: 181350.388 tau/day, 419.793 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 147733.999 tau/day, 341.977 timesteps/s
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10935 | 0.11844 | 0.12741 | 2.1 | 0.50
Neigh | 0.33 | 0.33945 | 0.35091 | 1.6 | 1.42
Comm | 0.49249 | 0.51745 | 0.53856 | 2.7 | 2.17
Output | 0.00053334 | 0.0007208 | 0.0007906 | 0.0 | 0.00
Modify | 22.82 | 22.822 | 22.825 | 0.0 | 95.81
Other | | 0.02289 | | | 0.10
Pair | 0.11648 | 0.1221 | 0.13001 | 1.5 | 0.42
Neigh | 0.34452 | 0.35618 | 0.36328 | 1.2 | 1.22
Comm | 0.63561 | 0.65617 | 0.67542 | 1.8 | 2.24
Output | 0.00056601 | 0.00069755 | 0.00074744 | 0.0 | 0.00
Modify | 28.069 | 28.076 | 28.082 | 0.1 | 96.01
Other | | 0.03094 | | | 0.11
Nlocal: 17.25 ave 23 max 10 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 506.5 ave 519 max 490 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 705.75 ave 998 max 369 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nlocal: 15 ave 16 max 14 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 437 ave 446 max 431 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 529 ave 595 max 437 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 2823
Ave neighs/atom = 40.913
Total # of neighbors = 2116
Ave neighs/atom = 35.2667
Neighbor list builds = 10000
Dangerous builds = 0
Total wall time: 0:00:23
Total wall time: 0:00:29

17
lib/kim/Install.py
View File

@ -21,7 +21,7 @@ Syntax from lib dir: python Install.py -b -v version -a kim-name
specify one or more options, order does not matter
-v = version of KIM API library to use
default = kim-api-v1.9.2 (current as of Oct 2017)
default = kim-api-v1.9.4 (current as of Apr 2018)
-b = download and build base KIM API library with example Models
this will delete any previous installation in the current folder
-n = do NOT download and build base KIM API library.
@ -109,7 +109,7 @@ nargs = len(args)
if nargs == 0: error()
thisdir = os.environ['PWD']
version = "kim-api-v1.9.2"
version = "kim-api-v1.9.4"
buildflag = False
everythingflag = False
@ -166,9 +166,6 @@ if pathflag:
mkfile.write("print_dir:\n")
mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir))
else:
kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version)
@ -191,9 +188,6 @@ if buildflag:
mkfile.write("print_dir:\n")
mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir))
# download entire kim-api tarball
@ -247,11 +241,16 @@ if buildflag:
# add single OpenKIM model
if addflag:
makefile_path = os.path.join(thisdir, "Makefile.KIM_DIR")
if os.path.isfile(makefile_path):
cmd = 'make --no-print-directory -f %s print_dir' % makefile_path
kimdir = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if not os.path.isdir(kimdir):
print("\nkim-api is not installed")
error()
# download single model
cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir, addmodelname)
cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print (txt.decode("UTF-8"))

36
lib/kim/README
View File

@ -20,47 +20,35 @@ Instructions:
1. Configure lammps for use with the kim-api library installed in this directory
$ printf "KIM_INSTALL_DIR=${PWD}\n" > ./Makefile.KIM_DIR
$ printf "include ${PWD}/lib/kim-api/Makefile.KIM_Config\n" > ./Makefile.KIM_Config
# replace X.Y.Z as appropriate here and below
$ printf "KIM_INSTALL_DIR=${PWD}/installed-kim-api-vX.Y.Z\n" > ./Makefile.KIM_DIR
2. Download and unpack the kim-api
# replace X.Y.Z as appropriate here and below
$ wget http://s3.openkim.org/kim-api/kim-api-vX.Y.Z.tgz
$ tar zxvf kim-api-vX.Y.Z.tgz
$ wget http://s3.openkim.org/kim-api/kim-api-vX.Y.Z.txz
$ tar zxvf kim-api-vX.Y.Z.txz
# configure the kim-api
$ cd kim-api-vX.Y.Z
$ ./configure --prefix=${PWD}/../
# setup the desired kim item
$ make add-Pair_Johnson_Fe__MO_857282754307_002
$ ./configure --prefix=${PWD}/../installed-kim-api-vX.Y.Z
3. Build and install the kim-api and model
$ make
$ make install
# replace X with the KIM API major version number
$ make install-set-default-to-vX
$ cd ../
$ cd ..
4. Remove source and build files
$ rm -rf kim-api-vX.Y.Z
$ rm -rf kim-api-vX.Y.Z.tgz
$ rm -rf kim-api-vX.Y.Z.txz
5. To add additional items do the following (replace the kim item name with your
5. To add items do the following (replace the kim item name with your
desired value)
$ wget https://openkim.org/download/EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz
$ tar zxvf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz
$ cd EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001
$ make
$ make install
$ cd ..
$ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001
$ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz
$ source ${PWD}/kim-api-vX.Y.Z/bin/kim-api-v1-activate
$ kim-api-v1-collections-management install system Pair_Johnson_Fe__MO_857282754307_002
-----------------
@ -73,4 +61,4 @@ $ make g++ (or whatever target you wish)
Note that the Makefile.lammps and Makefile.KIM_DIR files in this directory
are required to allow the LAMMPS build to find the necessary KIM files.
You should not normally need to edit this file.
You should not normally need to edit these files.

6
lib/kim/pair-kim.release.info
View File

@ -1,6 +0,0 @@
This package (pair-kim-v1.7.2+1) created from commit
ced1275c5fd5b382cb9bd39e44ed1324c7c85e99
of the pair-kim git repository
By Ryan S. Elliott (relliott@umn.edu) on Mon Feb 22 14:59:53 CST 2016.

28
lib/latte/Install.py
View File

@ -10,17 +10,21 @@ import sys,os,re,subprocess
help = """
Syntax from src dir: make lib-latte args="-b"
make lib-latte args="-p /usr/local/latte"
make lib-latte args="-m gfortran"
or: make lib-latte args="-p /usr/local/latte"
or: make lib-latte args="-m gfortran"
or: make lib-latte args="-b -v 1.1.1"
Syntax from lib dir: python Install.py -b
python Install.py -p /usr/local/latte
python Install.py -m gfortran
or: python Install.py -p /usr/local/latte
or: python Install.py -m gfortran
or: python Install.py -v 1.1.1 -b
specify one or more options, order does not matter
-b = download and build the LATTE library
-p = specify folder of existing LATTE installation
-m = copy Makefile.lammps.suffix to Makefile.lammps
-v = set version of LATTE library to download and set up (default = 1.1.1)
Example:
@ -30,7 +34,7 @@ make lib-latte args="-p $HOME/latte" # use existing LATTE installation
# settings
url = "https://github.com/lanl/LATTE/archive/master.tar.gz"
version = '1.1.1'
# print error message or help
@ -94,7 +98,6 @@ nargs = len(args)
if nargs == 0: error()
homepath = "."
homedir = "LATTE-master"
buildflag = False
pathflag = False
@ -116,12 +119,19 @@ while iarg < nargs:
suffix = args[iarg+1]
suffixflag = True
iarg += 2
elif args[iarg] == "-v":
if iarg+2 > nargs: error()
version = args[iarg+1]
iarg += 2
else: error()
homedir = "LATTE-%s" % version
if (buildflag and pathflag):
error("Cannot use -b and -p flag at the same time")
if buildflag:
url = "https://github.com/lanl/LATTE/archive/v%s.tar.gz" % version
lattepath = fullpath(homepath)
lattedir = "%s/%s" % (lattepath,homedir)
@ -132,15 +142,15 @@ if pathflag:
if buildflag:
print("Downloading LATTE ...")
geturl(url,"master.tar.gz")
geturl(url,"LATTE.tar.gz")
print("Unpacking LATTE zipfile ...")
if os.path.exists(lattedir):
cmd = 'rm -rf "%s"' % lattedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
cmd = 'cd "%s"; tar zxvf master.tar.gz' % lattepath
cmd = 'cd "%s"; tar zxvf LATTE.tar.gz' % lattepath
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
os.remove("%s/master.tar.gz" % lattepath)
os.remove("%s/LATTE.tar.gz" % lattepath)
# build LATTE

8
src/DIPOLE/pair_lj_long_dipole_long.h
View File

@ -113,13 +113,13 @@ E: Pair style requires use of kspace_style ewald/disp
Self-explanatory.
E: Pair style lj/long/dipole/long does not currently support respa
This feature is not yet supported.
E: Pair cutoff < Respa interior cutoff
One or more pairwise cutoffs are too short to use with the specified
rRESPA cutoffs.
U: Pair style lj/long/dipole/long does not currently support respa
This feature is not yet supported.
*/

5
src/GPU/fix_gpu.h
View File

@ -50,11 +50,6 @@ class FixGPU : public Fix {
/* ERROR/WARNING messages:
E: Cannot use GPU package with USER-CUDA package enabled
You cannot use both the GPU and USER-CUDA packages
together. Use one or the other.
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the

13
src/GPU/pair_tersoff_mod_gpu.h
View File

@ -54,14 +54,21 @@ E: Insufficient memory on accelerator
There is insufficient memory on one of the devices specified for the gpu
package
E: Pair style tersoff/gpu requires newton pair off
E: Pair style tersoff/mod/gpu requires atom IDs
See the newton command. This is a restriction to use this pair style.
UNDOCUMENTED
E: Pair style tersoff/mod/gpu requires newton pair off
UNDOCUMENTED
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
*/
U: Pair style tersoff/gpu requires newton pair off
See the newton command. This is a restriction to use this pair style.
*/

13
src/GPU/pair_tersoff_zbl_gpu.h
View File

@ -54,14 +54,21 @@ E: Insufficient memory on accelerator
There is insufficient memory on one of the devices specified for the gpu
package
E: Pair style tersoff/gpu requires newton pair off
E: Pair style tersoff/zbl/gpu requires atom IDs
See the newton command. This is a restriction to use this pair style.
UNDOCUMENTED
E: Pair style tersoff/zbl/gpu requires newton pair off
UNDOCUMENTED
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
*/
U: Pair style tersoff/gpu requires newton pair off
See the newton command. This is a restriction to use this pair style.
*/

8
src/GPU/pppm_gpu.h
View File

@ -102,4 +102,12 @@ outside a processor's sub-domain or even the entire simulation box.
This indicates bad physics, e.g. due to highly overlapping atoms, too
large a timestep, etc.
E: Cannot (yet) use K-space slab correction with compute group/group for triclinic systems
UNDOCUMENTED
E: Cannot (yet) use kspace_modify diff ad with compute group/group
UNDOCUMENTED
*/

10
src/GRANULAR/fix_wall_gran.h
View File

@ -101,6 +101,10 @@ E: Fix wall/gran requires atom style sphere
Self-explanatory.
E: Invalid fix wall/gran interaction style
UNDOCUMENTED
E: Cannot use wall in periodic dimension
Self-explanatory.
@ -117,7 +121,11 @@ E: Invalid shear direction for fix wall/gran
Self-explanatory.
E: Fix wall/gran is incompatible with Pair style
E: Cannot wiggle or shear with fix wall/gran/region
UNDOCUMENTED
U: Fix wall/gran is incompatible with Pair style
Must use a granular pair style to define the parameters needed for
this fix.

30
src/GRANULAR/fix_wall_gran_region.h
View File

@ -71,33 +71,49 @@ class FixWallGranRegion : public FixWallGran {
/* ERROR/WARNING messages:
E: Illegal ... command
E: Region ID for fix wall/gran/region does not exist
UNDOCUMENTED
W: Region properties for region %s changed between runs, resetting its motion
UNDOCUMENTED
W: Region properties for region %s are inconsistent with restart file, resetting its motion
UNDOCUMENTED
E: Too many wall/gran/region contacts for one particle
UNDOCUMENTED
U: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Fix wall/gran requires atom style sphere
U: Fix wall/gran requires atom style sphere
Self-explanatory.
E: Cannot use wall in periodic dimension
U: Cannot use wall in periodic dimension
Self-explanatory.
E: Cannot wiggle and shear fix wall/gran
U: Cannot wiggle and shear fix wall/gran
Cannot specify both options at the same time.
E: Invalid wiggle direction for fix wall/gran
U: Invalid wiggle direction for fix wall/gran
Self-explanatory.
E: Invalid shear direction for fix wall/gran
U: Invalid shear direction for fix wall/gran
Self-explanatory.
E: Fix wall/gran is incompatible with Pair style
U: Fix wall/gran is incompatible with Pair style
Must use a granular pair style to define the parameters needed for
this fix.

8
src/GRANULAR/pair_gran_hooke_history.h
View File

@ -90,12 +90,16 @@ E: Pair granular requires ghost atoms store velocity
Use the comm_modify vel yes command to enable this.
E: Pair granular with shear history requires newton pair off
E: Could not find pair fix neigh history ID
UNDOCUMENTED
U: Pair granular with shear history requires newton pair off
This is a current restriction of the implementation of pair
granular styles with history.
E: Could not find pair fix ID
U: Could not find pair fix ID
A fix is created internally by the pair style to store shear
history information. You cannot delete it.

13
src/KIM/pair_kim.cpp
View File

@ -27,7 +27,6 @@
// includes from LAMMPS
#include "pair_kim.h"
#include "pair_kim_version.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
@ -1094,18 +1093,6 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
"#\n"
"# This file is automatically generated from LAMMPS pair_style "
"kim command\n");
char tmp_version[100];
sprintf(tmp_version,"# This is pair-kim-v%i.%i.%i",
PAIR_KIM_VERSION_MAJOR, PAIR_KIM_VERSION_MINOR,
PAIR_KIM_VERSION_PATCH);
strcat(*test_descriptor_string, tmp_version);
#ifdef PAIR_KIM_VERSION_PRERELEASE
sprintf(tmp_version,"-%s", PAIR_KIM_VERSION_PRERELEASE);
strcat(*test_descriptor_string, tmp_version);
#endif
#ifdef PAIR_KIM_VERSION_BUILD_METADATA
sprintf(tmp_version,"+%s", PAIR_KIM_VERSION_BUILD_METADATA);
#endif
strcat(*test_descriptor_string,
"\n"
"# The call number is (pair_style).(init_style): ");

32
src/KIM/pair_kim.h
View File

@ -197,24 +197,40 @@ E: Unknown unit_style
Self-explanatory. Check the input script or data file.
W: KIM Model does not provide 'energy'; Potential energy will be zero
W: KIM Model does not provide `energy'; Potential energy will be zero
Self-explanatory.
UNDOCUMENTED
W: KIM Model does not provide 'forces'; Forces will be zero
W: KIM Model does not provide `forces'; Forces will be zero
Self-explanatory.
UNDOCUMENTED
W: KIM Model does not provide 'particleEnergy'; energy per atom will be zero
W: KIM Model does not provide `particleEnergy'; energy per atom will be zero
Self-explanatory.
UNDOCUMENTED
W: KIM Model does not provide 'particleVirial'; virial per atom will be zero
W: KIM Model does not provide `particleVirial'; virial per atom will be zero
Self-explanatory.
UNDOCUMENTED
E: Test_descriptor_string already allocated
This is an internal error. Contact the developers.
U: KIM Model does not provide 'energy'; Potential energy will be zero
Self-explanatory.
U: KIM Model does not provide 'forces'; Forces will be zero
Self-explanatory.
U: KIM Model does not provide 'particleEnergy'; energy per atom will be zero
Self-explanatory.
U: KIM Model does not provide 'particleVirial'; virial per atom will be zero
Self-explanatory.
*/

64
src/KIM/pair_kim_version.h
View File

@ -1,64 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Ryan S. Elliott,
------------------------------------------------------------------------- */
#ifndef LMP_PAIR_KIM_VERSION_H
#define LMP_PAIR_KIM_VERSION_H
//
// Release: This file is part of the pair-kim-v1.7.2+1 package.
//
//
// This file defines the version information for the pair-kim package.
// The values specified here must conform to the Semantic Versioning
// 2.0.0 specification.
//
// Generally the version numbering for the pair-kim package will
// parallel the numbering for the kim-api package. However, if
// additional versioning increments are required for the pair-kim
// package, the build-metatdata field will be used to provide a
// "sub-patch" version number.
//
// The PATCH value should be incremented IMMEDIATELY after an official
// release.
//
// The MINOR value should be incremented AND the PATCH value reset to
// zero as soon as it becomes clear that the next official release
// MUST increment the MINOR version value.
//
// The MAJOR value should be incremented AND the MINOR and PATCH
// vaules reset to zero as soon as it becomes clear that the next
// official release MUST increment the MAJOR version value.
//
// The PRERELEASE value can be set to any value allowed by the
// Semantic Versioning specification. However, it will generally be
// empty. This value should be quoted as a string constant.
//
// The BUILD_METADATA value can be set to any value allowed by the
// Semantic Versioning specification. However, it will generally be
// emtpy; Except for when "sub-patch" versioning of the pair-kim
// package is necessary. This value should be quoted as a string
// constant.
//
#define PAIR_KIM_VERSION_MAJOR 1
#define PAIR_KIM_VERSION_MINOR 7
#define PAIR_KIM_VERSION_PATCH 2
//#define PAIR_KIM_VERSION_PRERELEASE
#define PAIR_KIM_VERSION_BUILD_METADATA "1"
#endif /* PAIR_KIM_VERSION_H */

10
src/KOKKOS/atom_vec_hybrid_kokkos.h
View File

@ -154,7 +154,15 @@ E: Per-processor system is too big
The number of owned atoms plus ghost atoms on a single
processor must fit in 32-bit integer.
E: Invalid atom type in Atoms section of data file
E: AtomVecHybridKokkos doesn't yet support threaded comm
UNDOCUMENTED
E: Invalid atom h_type in Atoms section of data file
UNDOCUMENTED
U: Invalid atom type in Atoms section of data file
Atom types must range from 1 to specified # of types.

6
src/KOKKOS/improper_class2_kokkos.h
View File

@ -107,7 +107,11 @@ class ImproperClass2Kokkos : public ImproperClass2 {
/* ERROR/WARNING messages:
W: Dihedral problem
W: Improper problem
UNDOCUMENTED
U: Dihedral problem
Conformation of the 4 listed dihedral atoms is extreme; you may want
to check your simulation geometry.

2
src/KOKKOS/kokkos.h
View File

@ -67,7 +67,7 @@ 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: Must use Kokkos half/thread or full neighbor list with threads or GPUs
U: Must use Kokkos half/thread or full neighbor list with threads or GPUs
Using Kokkos half-neighbor lists with threading is not allowed.

29
src/KOKKOS/pair_reaxc_kokkos.cpp
View File

@ -89,6 +89,17 @@ PairReaxCKokkos<DeviceType>::~PairReaxCKokkos()
tmpid = NULL;
memoryKK->destroy_kokkos(k_tmpbo,tmpbo);
tmpbo = NULL;
// deallocate views of views in serial to prevent race condition in profiling tools
for (int i = 0; i < k_LR.extent(0); i++) {
for (int j = 0; j < k_LR.extent(1); j++) {
k_LR.h_view(i,j).d_vdW = decltype(k_LR.h_view(i,j).d_vdW )();
k_LR.h_view(i,j).d_CEvd = decltype(k_LR.h_view(i,j).d_CEvd )();
k_LR.h_view(i,j).d_ele = decltype(k_LR.h_view(i,j).d_ele )();
k_LR.h_view(i,j).d_CEclmb = decltype(k_LR.h_view(i,j).d_CEclmb)();
}
}
}
/* ---------------------------------------------------------------------- */
@ -376,47 +387,31 @@ void PairReaxCKokkos<DeviceType>::init_md()
for (int j = i; j <= ntypes; ++j) {
int n = LR[i][j].n;
if (n == 0) continue;
k_LR.h_view(i,j).xmin = LR[i][j].xmin;
k_LR.h_view(i,j).xmax = LR[i][j].xmax;
k_LR.h_view(i,j).n = LR[i][j].n;
k_LR.h_view(i,j).dx = LR[i][j].dx;
k_LR.h_view(i,j).inv_dx = LR[i][j].inv_dx;
k_LR.h_view(i,j).a = LR[i][j].a;
k_LR.h_view(i,j).m = LR[i][j].m;
k_LR.h_view(i,j).c = LR[i][j].c;
typename LR_lookup_table_kk<DeviceType>::tdual_LR_data_1d k_y = typename LR_lookup_table_kk<DeviceType>::tdual_LR_data_1d("lookup:LR[i,j].y",n);
typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d k_H = typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d("lookup:LR[i,j].H",n);
typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d k_vdW = typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d("lookup:LR[i,j].vdW",n);
typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d k_CEvd = typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d("lookup:LR[i,j].CEvd",n);
typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d k_ele = typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d("lookup:LR[i,j].ele",n);
typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d k_CEclmb = typename LR_lookup_table_kk<DeviceType>::tdual_cubic_spline_coef_1d("lookup:LR[i,j].CEclmb",n);
k_LR.h_view(i,j).d_y = k_y.template view<DeviceType>();
k_LR.h_view(i,j).d_H = k_H.template view<DeviceType>();
k_LR.h_view(i,j).d_vdW = k_vdW.template view<DeviceType>();
k_LR.h_view(i,j).d_CEvd = k_CEvd.template view<DeviceType>();
k_LR.h_view(i,j).d_ele = k_ele.template view<DeviceType>();
k_LR.h_view(i,j).d_CEclmb = k_CEclmb.template view<DeviceType>();
for (int k = 0; k < n; k++) {
k_y.h_view(k) = LR[i][j].y[k];
k_H.h_view(k) = LR[i][j].H[k];
k_vdW.h_view(k) = LR[i][j].vdW[k];
k_CEvd.h_view(k) = LR[i][j].CEvd[k];
k_ele.h_view(k) = LR[i][j].ele[k];
k_CEclmb.h_view(k) = LR[i][j].CEclmb[k];
}
k_y.template modify<LMPHostType>();
k_H.template modify<LMPHostType>();
k_vdW.template modify<LMPHostType>();
k_CEvd.template modify<LMPHostType>();
k_ele.template modify<LMPHostType>();
k_CEclmb.template modify<LMPHostType>();
k_y.template sync<DeviceType>();
k_H.template sync<DeviceType>();
k_vdW.template sync<DeviceType>();
k_CEvd.template sync<DeviceType>();
k_ele.template sync<DeviceType>();
@ -1216,7 +1211,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTabulatedLJCoulomb<N
const int tmin = MIN( itype, jtype );
const int tmax = MAX( itype, jtype );
const LR_lookup_table_kk<DeviceType> t = d_LR(tmin,tmax);
const LR_lookup_table_kk<DeviceType>& t = d_LR(tmin,tmax);
/* Cubic Spline Interpolation */

10
src/KOKKOS/pair_reaxc_kokkos.h
View File

@ -42,21 +42,11 @@ namespace LAMMPS_NS {
template<class DeviceType>
struct LR_lookup_table_kk
{
typedef Kokkos::DualView<LR_data*,Kokkos::LayoutRight,DeviceType> tdual_LR_data_1d;
typedef typename tdual_LR_data_1d::t_dev t_LR_data_1d;
typedef Kokkos::DualView<cubic_spline_coef*,Kokkos::LayoutRight,DeviceType> tdual_cubic_spline_coef_1d;
typedef typename tdual_cubic_spline_coef_1d::t_dev t_cubic_spline_coef_1d;
double xmin, xmax;
int n;
double dx, inv_dx;
double a;
double m;
double c;
t_LR_data_1d d_y;
t_cubic_spline_coef_1d d_H;
t_cubic_spline_coef_1d d_vdW, d_CEvd;
t_cubic_spline_coef_1d d_ele, d_CEclmb;
};

62
src/KOKKOS/pair_table_kokkos.h
View File

@ -187,14 +187,6 @@ class PairTableKokkos : public PairTable {
/* ERROR/WARNING messages:
E: Pair distance < table inner cutoff
Two atoms are closer together than the pairwise table allows.
E: Pair distance > table outer cutoff
Two atoms are further apart than the pairwise table allows.
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
@ -209,54 +201,62 @@ E: Illegal number of pair table entries
There must be at least 2 table entries.
E: Invalid pair table length
Length of read-in pair table is invalid
E: Invalid pair table cutoff
Cutoffs in pair_coeff command are not valid with read-in pair table.
E: Bitmapped table in file does not match requested table
Setting for bitmapped table in pair_coeff command must match table
in file exactly.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Cannot open file %s
E: Cannot use chosen neighbor list style with lj/cut/kk
That style is not supported by Kokkos.
U: Pair distance < table inner cutoff
Two atoms are closer together than the pairwise table allows.
U: Pair distance > table outer cutoff
Two atoms are further apart than the pairwise table allows.
U: Invalid pair table length
Length of read-in pair table is invalid
U: Invalid pair table cutoff
Cutoffs in pair_coeff command are not valid with read-in pair table.
U: Bitmapped table in file does not match requested table
Setting for bitmapped table in pair_coeff command must match table
in file exactly.
U: Cannot open file %s
The specified file cannot be opened. Check that the path and name are
correct. If the file is a compressed file, also check that the gzip
executable can be found and run.
E: Did not find keyword in table file
U: Did not find keyword in table file
Keyword used in pair_coeff command was not found in table file.
E: Bitmapped table is incorrect length in table file
U: Bitmapped table is incorrect length in table file
Number of table entries is not a correct power of 2.
E: Invalid keyword in pair table parameters
U: Invalid keyword in pair table parameters
Keyword used in list of table parameters is not recognized.
E: Pair table parameters did not set N
U: Pair table parameters did not set N
List of pair table parameters must include N setting.
E: Pair table cutoffs must all be equal to use with KSpace
U: Pair table cutoffs must all be equal to use with KSpace
When using pair style table with a long-range KSpace solver, the
cutoffs for all atom type pairs must all be the same, since the
long-range solver starts at that cutoff.
E: Cannot use chosen neighbor list style with lj/cut/kk
That style is not supported by Kokkos.
*/

20
src/KOKKOS/pair_yukawa_kokkos.h
View File

@ -129,18 +129,22 @@ class PairYukawaKokkos : public PairYukawa {
/* ERROR/WARNING messages:
E: Illegal ... command
E: Cannot use Kokkos pair style with rRESPA inner/middle
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: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
UNDOCUMENTED
E: Cannot use chosen neighbor list style with yukawa/kk
That style is not supported by Kokkos.
U: Illegal ... command
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.
U: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
*/

8
src/KOKKOS/pair_zbl_kokkos.h
View File

@ -110,4 +110,12 @@ class PairZBLKokkos : public PairZBL {
/* ERROR/WARNING messages:
E: Cannot use Kokkos pair style with rRESPA inner/middle
UNDOCUMENTED
E: Cannot use chosen neighbor list style with lj/cut/kk
UNDOCUMENTED
*/

70
src/KOKKOS/pppm_kokkos.h
View File

@ -432,9 +432,9 @@ 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: Cannot (yet) use PPPM with triclinic box and kspace_modify diff ad
E: Cannot (yet) use PPPM Kokkos with 'kspace_modify diff ad'
This feature is not yet supported.
UNDOCUMENTED
E: Cannot (yet) use PPPM with triclinic box and slab correction
@ -449,9 +449,9 @@ E: PPPM can only currently be used with comm_style brick
This is a current restriction in LAMMPS.
E: Kspace style requires atom attribute q
E: Kspace style requires atomKK attribute q
The atom style defined does not have these attributes.
UNDOCUMENTED
E: Cannot use nonperiodic boundaries with PPPM
@ -473,26 +473,9 @@ E: KSpace style is incompatible with Pair style
Setting a kspace style requires that a pair style with matching
long-range Coulombic or dispersion components be used.
E: Pair style is incompatible with TIP4P KSpace style
E: Cannot (yet) use PPPM Kokkos TIP4P
The pair style does not have the requires TIP4P settings.
E: Bond and angle potentials must be defined for TIP4P
Cannot use TIP4P pair potential unless bond and angle potentials
are defined.
E: Bad TIP4P angle type for PPPM/TIP4P
Specified angle type is not valid.
E: Bad TIP4P bond type for PPPM/TIP4P
Specified bond type is not valid.
E: Cannot (yet) use PPPM with triclinic box and TIP4P
This feature is not yet supported.
UNDOCUMENTED
W: Reducing PPPM order b/c stencil extends beyond nearest neighbor processor
@ -512,11 +495,9 @@ E: KSpace accuracy must be > 0
The kspace accuracy designated in the input must be greater than zero.
E: Could not compute grid size
E: Must use 'kspace_modify gewald' for uncharged system
The code is unable to compute a grid size consistent with the desired
accuracy. This error should not occur for typical problems. Please
send an email to the developers.
UNDOCUMENTED
E: PPPM grid is too large
@ -550,4 +531,39 @@ outside a processor's sub-domain or even the entire simulation box.
This indicates bad physics, e.g. due to highly overlapping atoms, too
large a timestep, etc.
U: Cannot (yet) use PPPM with triclinic box and kspace_modify diff ad
This feature is not yet supported.
U: Kspace style requires atom attribute q
The atom style defined does not have these attributes.
U: Pair style is incompatible with TIP4P KSpace style
The pair style does not have the requires TIP4P settings.
U: Bond and angle potentials must be defined for TIP4P
Cannot use TIP4P pair potential unless bond and angle potentials
are defined.
U: Bad TIP4P angle type for PPPM/TIP4P
Specified angle type is not valid.
U: Bad TIP4P bond type for PPPM/TIP4P
Specified bond type is not valid.
U: Cannot (yet) use PPPM with triclinic box and TIP4P
This feature is not yet supported.
U: Could not compute grid size
The code is unable to compute a grid size consistent with the desired
accuracy. This error should not occur for typical problems. Please
send an email to the developers.
*/

4
src/KSPACE/ewald.h
View File

@ -122,6 +122,10 @@ E: KSpace accuracy must be > 0
The kspace accuracy designated in the input must be greater than zero.
E: Must use 'kspace_modify gewald' for uncharged system
UNDOCUMENTED
E: Cannot (yet) use K-space slab correction with compute group/group for triclinic systems
This option is not yet supported.

8
src/KSPACE/ewald_disp.h
View File

@ -146,6 +146,14 @@ W: System is not charge neutral, net charge = %g
The total charge on all atoms on the system is not 0.0.
For some KSpace solvers this is only a warning.
E: KSpace accuracy must be > 0
UNDOCUMENTED
E: Must use 'kspace_modify gewald' for uncharged system
UNDOCUMENTED
W: Ewald/disp Newton solver failed, using old method to estimate g_ewald
Self-explanatory. Choosing a different cutoff value may help.

8
src/KSPACE/pair_buck_long_coul_long.h
View File

@ -101,9 +101,9 @@ E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style buck/long/coul/long requires atom attribute q
E: Invoking coulombic in pair style buck/long/coul/long requires atom attribute q
The atom style defined does not have this attribute.
UNDOCUMENTED
E: Pair style requires a KSpace style
@ -119,4 +119,8 @@ E: Pair cutoff < Respa interior cutoff
One or more pairwise cutoffs are too short to use with the specified
rRESPA cutoffs.
U: Pair style buck/long/coul/long requires atom attribute q
The atom style defined does not have this attribute.
*/

8
src/KSPACE/pair_lj_long_coul_long.h
View File

@ -97,9 +97,9 @@ E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Invoking coulombic in pair style lj/coul requires atom attribute q
E: Invoking coulombic in pair style lj/long/coul/long requires atom attribute q
The atom style defined does not have this attribute.
UNDOCUMENTED
E: Pair style requires a KSpace style
@ -110,4 +110,8 @@ E: Pair cutoff < Respa interior cutoff
One or more pairwise cutoffs are too short to use with the specified
rRESPA cutoffs.
U: Invoking coulombic in pair style lj/coul requires atom attribute q
The atom style defined does not have this attribute.
*/

16
src/KSPACE/pppm.h
View File

@ -209,6 +209,10 @@ 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: Must redefine kspace_style after changing to triclinic box
UNDOCUMENTED
E: Cannot (yet) use PPPM with triclinic box and kspace_modify diff ad
This feature is not yet supported.
@ -267,10 +271,6 @@ E: Bad TIP4P bond type for PPPM/TIP4P
Specified bond type is not valid.
E: Cannot (yet) use PPPM with triclinic box and TIP4P
This feature is not yet supported.
W: Reducing PPPM order b/c stencil extends beyond nearest neighbor processor
This may lead to a larger grid than desired. See the kspace_modify overlap
@ -289,6 +289,10 @@ E: KSpace accuracy must be > 0
The kspace accuracy designated in the input must be greater than zero.
E: Must use kspace_modify gewald for uncharged system
UNDOCUMENTED
E: Could not compute grid size
The code is unable to compute a grid size consistent with the desired
@ -335,4 +339,8 @@ E: Cannot (yet) use kspace_modify diff ad with compute group/group
This option is not yet supported.
U: Cannot (yet) use PPPM with triclinic box and TIP4P
This feature is not yet supported.
*/

44
src/LATTE/fix_latte.h
View File

@ -64,10 +64,54 @@ class FixLatte : public Fix {
/* ERROR/WARNING messages:
E: Must use units metal with fix latte command
UNDOCUMENTED
E: Fix latte currently runs only in serial
UNDOCUMENTED
E: LAMMPS is linked against incompatible LATTE library
UNDOCUMENTED
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Fix latte does not yet support a LAMMPS calculation of a Coulomb potential
UNDOCUMENTED
E: Could not find fix latte compute ID
UNDOCUMENTED
E: Fix latte compute ID does not compute pe/atom
UNDOCUMENTED
E: Fix latte requires 3d problem
UNDOCUMENTED
E: Fix latte cannot compute Coulomb potential
UNDOCUMENTED
E: Fix latte requires 3d simulation
UNDOCUMENTED
W: Fix latte should come after all other integration fixes
UNDOCUMENTED
E: Internal LATTE problem
UNDOCUMENTED
*/

2
src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
View File

@ -23,7 +23,7 @@ ARCHIVE = ar
ARFLAGS = -rc
SHLIBFLAGS = -shared
KOKKOS_DEVICES = Cuda
KOKKOS_ARCH = Kepler35
KOKKOS_ARCH = Kepler35
# ---------------------------------------------------------------------
# LAMMPS-specific settings, all OPTIONAL

4
src/MANYBODY/pair_bop.h
View File

@ -286,4 +286,8 @@ E: Incorrect table format check for element types
Self-explanatory.
E: Unsupported BOP potential file format
UNDOCUMENTED
*/

4
src/MANYBODY/pair_eam.h
View File

@ -134,4 +134,8 @@ E: Cannot open EAM potential file %s
The specified EAM potential file cannot be opened. Check that the
path and name are correct.
E: Invalid EAM potential file
UNDOCUMENTED
*/

4
src/MANYBODY/pair_eam_alloy.h
View File

@ -62,4 +62,8 @@ E: Incorrect element names in EAM potential file
The element names in the EAM file do not match those requested.
E: Invalid EAM potential file
UNDOCUMENTED
*/

4
src/MANYBODY/pair_eam_fs.h
View File

@ -62,4 +62,8 @@ E: Incorrect element names in EAM potential file
The element names in the EAM file do not match those requested.
E: Invalid EAM potential file
UNDOCUMENTED
*/

3
src/MANYBODY/pair_gw.cpp
View File

@ -521,7 +521,8 @@ void PairGW::setup_params()
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
if (n >= 0)
error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}

6
src/MANYBODY/pair_gw.h
View File

@ -185,12 +185,10 @@ invalid.
E: Potential file has duplicate entry
The potential file for a SW or GW potential has more than
one entry for the same 3 ordered elements.
The potential file has more than one entry for the same element.
E: Potential file is missing an entry
The potential file for a SW or GW potential does not have a
needed entry.
The potential file does not have a needed entry.
*/

8
src/MANYBODY/pair_gw_zbl.h
View File

@ -51,9 +51,9 @@ class PairGWZBL : public PairGW {
/* ERROR/WARNING messages:
E: Pair GW/zbl requires metal or real units
E: Pair gw/zbl requires metal or real units
This is a current restriction of this pair potential.
UNDOCUMENTED
E: Cannot open GW potential file %s
@ -69,4 +69,8 @@ E: Illegal GW parameter
One or more of the coefficients defined in the potential file is
invalid.
U: Pair GW/zbl requires metal or real units
This is a current restriction of this pair potential.
*/

8
src/MANYBODY/pair_polymorphic.h
View File

@ -358,4 +358,12 @@ E: Element not defined in potential file
The specified element is not in the potential file.
E: Potential file incompatible with this pair style version
UNDOCUMENTED
E: Error reading potential file header
UNDOCUMENTED
*/

4
src/MANYBODY/pair_tersoff_mod_c.h
View File

@ -55,11 +55,11 @@ E: Illegal Tersoff parameter
One or more of the coefficients defined in the potential file is
invalid.
E: Potential file has duplicate entry
U: Potential file has duplicate entry
The potential file has more than one entry for the same element.
E: Potential file is missing an entry
U: Potential file is missing an entry
The potential file does not have a needed entry.

22
src/MANYBODY/pair_vashishta_table.h
View File

@ -57,43 +57,47 @@ 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: Incorrect args for pair coefficients
E: Illegal inner cutoff for tabulation
UNDOCUMENTED
U: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style Vashishta requires atom IDs
U: Pair style Vashishta requires atom IDs
This is a requirement to use the Vashishta potential.
E: Pair style Vashishta requires newton pair on
U: Pair style Vashishta requires newton pair on
See the newton command. This is a restriction to use the Vashishta
potential.
E: All pair coeffs are not set
U: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Cannot open Vashishta potential file %s
U: Cannot open Vashishta potential file %s
The specified Vashishta potential file cannot be opened. Check that the path
and name are correct.
E: Incorrect format in Vashishta potential file
U: Incorrect format in Vashishta potential file
Incorrect number of words per line in the potential file.
E: Illegal Vashishta parameter
U: Illegal Vashishta parameter
One or more of the coefficients defined in the potential file is
invalid.
E: Potential file has duplicate entry
U: Potential file has duplicate entry
The potential file has more than one entry for the same element.
E: Potential file is missing an entry
U: Potential file is missing an entry
The potential file does not have a needed entry.

10
src/MC/fix_gcmc.cpp
View File

@ -686,7 +686,7 @@ void FixGCMC::init()
// warning if group id is "all"
if (groupbit & 1)
if ((comm->me == 0) && (groupbit & 1))
error->warning(FLERR, "Fix gcmc is being applied "
"to the default group all");
@ -1253,6 +1253,10 @@ void FixGCMC::attempt_molecule_deletion()
if (ngas == 0) return;
// work-around to avoid n=0 problem with fix rigid/nvt/small
if (ngas == natoms_per_molecule) return;
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;
@ -1910,6 +1914,10 @@ void FixGCMC::attempt_molecule_deletion_full()
if (ngas == 0) return;
// work-around to avoid n=0 problem with fix rigid/nvt/small
if (ngas == natoms_per_molecule) return;
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;

58
src/MC/fix_gcmc.h
View File

@ -197,10 +197,26 @@ E: Fix gcmc atom has charge, but atom style does not
Self-explanatory.
E: Cannot use fix gcmc rigid and not molecule
UNDOCUMENTED
E: Cannot use fix gcmc shake and not molecule
Self-explanatory.
E: Cannot use fix gcmc rigid and shake
UNDOCUMENTED
E: Cannot use fix gcmc rigid with MC moves
UNDOCUMENTED
E: Cannot use fix gcmc shake with MC moves
UNDOCUMENTED
E: Molecule template ID for fix gcmc does not exist
Self-explanatory.
@ -222,17 +238,6 @@ included one or more of the following: kspace, a hybrid
pair style, an eam pair style, tail correction,
or no "single" function for the pair style.
W: Energy of old configuration in fix gcmc is > MAXENERGYTEST.
This probably means that a pair of atoms are closer than the
overlap cutoff distance for keyword overlap_cutoff.
W: Fix gcmc is being applied to the default group all
This is allowed, but it will result in Monte Carlo moves
being performed on all the atoms in the system, which is
often not what is intended.
E: Invalid atom type in fix gcmc command
The atom type specified in the gcmc command does not exist.
@ -256,6 +261,14 @@ Should not choose the gcmc molecule feature if no molecules are being
simulated. The general molecule flag is off, but gcmc's molecule flag
is on.
E: Fix gcmc rigid fix does not exist
UNDOCUMENTED
E: Fix gcmc and fix rigid/small not using same molecule template ID
UNDOCUMENTED
E: Fix gcmc shake fix does not exist
Self-explanatory.
@ -264,10 +277,6 @@ E: Fix gcmc and fix shake not using same molecule template ID
Self-explanatory.
E: Fix gcmc can not currently be used with fix rigid or fix rigid/small
Self-explanatory.
E: Cannot use fix gcmc in a 2d simulation
Fix gcmc is set up to run in 3d only. No 2d simulations with fix gcmc
@ -291,10 +300,25 @@ E: Cannot do GCMC on atoms in atom_modify first group
This is a restriction due to the way atoms are organized in a list to
enable the atom_modify first command.
W: Fix gcmc is being applied to the default group all
This is allowed, but it will result in Monte Carlo moves
being performed on all the atoms in the system, which is
often not what is intended.
E: Could not find specified fix gcmc group ID
Self-explanatory.
E: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process.
UNDOCUMENTED
W: Energy of old configuration in fix gcmc is > MAXENERGYTEST.
This probably means that a pair of atoms are closer than the
overlap cutoff distance for keyword overlap_cutoff.
E: Fix gcmc put atom outside box
This should not normally happen. Contact the developers.
@ -311,4 +335,8 @@ E: Too many total atoms
See the setting for bigint in the src/lmptype.h file.
U: Fix gcmc can not currently be used with fix rigid or fix rigid/small
Self-explanatory.
*/

4
src/MEAM/pair_meam.h
View File

@ -106,6 +106,10 @@ class PairMEAM : public Pair {
/* ERROR/WARNING messages:
W: The pair_style meam command is unsupported. Please use pair_style meam/c instead
UNDOCUMENTED
E: MEAM library error %d
A call to the MEAM Fortran library returned an error.

12
src/MISC/fix_deposit.h
View File

@ -137,9 +137,9 @@ E: Region ID for fix deposit does not exist
Self-explanatory.
E: Fix pour rigid fix does not exist
E: Fix deposit rigid fix does not exist
Self-explanatory.
UNDOCUMENTED
E: Fix deposit and fix rigid/small not using same molecule template ID
@ -159,6 +159,10 @@ This test is performed for finite size particles with a diameter, not
for point particles. The near setting is smaller than the particle
diameter which can lead to overlaps.
E: Unknown particle distribution in fix deposit
UNDOCUMENTED
W: Particle deposition was unsuccessful
The fix deposit command was not able to insert as many atoms as
@ -177,4 +181,8 @@ E: Molecule template ID for fix deposit does not exist
Self-explanatory.
U: Fix pour rigid fix does not exist
Self-explanatory.
*/

4
src/MOLECULE/angle_table.h
View File

@ -117,4 +117,8 @@ E: Angle table parameters did not set N
List of angle table parameters must include N setting.
E: Illegal angle in angle style table
UNDOCUMENTED
*/

24
src/MOLECULE/bond_table.h
View File

@ -110,6 +110,18 @@ E: Did not find keyword in table file
Keyword used in pair_coeff command was not found in table file.
E: Premature end of file in bond table
UNDOCUMENTED
W: %d of %d force values in table are inconsistent with -dE/dr.\n Should only be flagged at inflection points
UNDOCUMENTED
W: %d of %d lines in table were incomplete or could not be parsed completely
UNDOCUMENTED
E: Invalid keyword in bond table parameters
Self-explanatory.
@ -118,4 +130,16 @@ E: Bond table parameters did not set N
List of bond table parameters must include N setting.
E: Illegal bond in bond style table
UNDOCUMENTED
E: Bond length < table inner cutoff: type %d length %g
UNDOCUMENTED
E: Bond length > table outer cutoff: type %d length %g
UNDOCUMENTED
*/

12
src/MOLECULE/dihedral_charmm.h
View File

@ -69,6 +69,18 @@ E: Incorrect weight arg for dihedral coefficients
Self-explanatory. Check the input script or data file.
E: Dihedral style charmm must be set to same r-RESPA level as 'pair'
UNDOCUMENTED
E: Dihedral style charmm must be set to same r-RESPA level as 'outer'
UNDOCUMENTED
E: Must use 'special_bonds charmm' with dihedral style charmm for use with CHARMM pair styles
UNDOCUMENTED
E: Dihedral charmm is incompatible with Pair style
Dihedral style charmm must be used with a pair style charmm

12
src/MOLECULE/dihedral_charmmfsw.h
View File

@ -73,6 +73,18 @@ E: Incorrect weight arg for dihedral coefficients
Self-explanatory. Check the input script or data file.
E: Dihedral style charmmfsw must be set to same r-RESPA level as 'pair'
UNDOCUMENTED
E: Dihedral style charmmfsw must be set to same r-RESPA level as 'outer'
UNDOCUMENTED
E: Must use 'special_bonds charmm' with dihedral style charmm for use with CHARMM pair styles
UNDOCUMENTED
E: Dihedral charmmfsw is incompatible with Pair style
Dihedral style charmmfsw must be used with a pair style charmm

36
src/MOLECULE/fix_cmap.h
View File

@ -128,3 +128,39 @@ class FixCMAP : public Fix {
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
UNDOCUMENTED
E: CMAP atoms %d %d %d %d %d missing on proc %d at step %ld
UNDOCUMENTED
E: Invalid CMAP crossterm_type
UNDOCUMENTED
E: Cannot open fix cmap file %s
UNDOCUMENTED
E: CMAP: atan2 function cannot take 2 zero arguments
UNDOCUMENTED
E: Invalid read data header line for fix cmap
UNDOCUMENTED
E: Incorrect %s format in data file
UNDOCUMENTED
E: Too many CMAP crossterms for one atom
UNDOCUMENTED
*/

7
src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h
View File

@ -80,9 +80,12 @@ E: Pair style lj/charmmfsw/coul/charmmfsh requires atom attribute q
The atom style defined does not have these attributes.
E: Pair inner cutoff >= Pair outer cutoff
E: Pair inner lj cutoff >= Pair outer lj cutoff
UNDOCUMENTED
U: Pair inner cutoff >= Pair outer cutoff
The specified cutoffs for the pair style are inconsistent.
*/

10
src/MPIIO/dump_custom_mpiio.h
View File

@ -79,10 +79,9 @@ E: Too much per-proc info for dump
Number of local atoms times number of columns must fit in a 32-bit
integer for dump.
E: Dump_modify format string is too short
E: Dump_modify format line is too short
There are more fields to be dumped in a line of output than your
format string specifies.
UNDOCUMENTED
E: Could not find dump custom compute ID
@ -105,4 +104,9 @@ E: Region ID for dump custom does not exist
Self-explanatory.
U: Dump_modify format string is too short
There are more fields to be dumped in a line of output than your
format string specifies.
*/

32
src/MSCG/fix_mscg.h
View File

@ -59,19 +59,29 @@ Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Fix mscg does not yet support mpi
E: Fix mscg does not yet support parallel use via MPI
Self-explanatory.
UNDOCUMENTED
E: Fix mscg must be used with 32-bit atom IDs
UNDOCUMENTED
E: Fix mscg does not yet support triclinic geometries
Self-explanatory.
E: Bond/Angle/Dihedral list overflow, boost fix_mscg max
E: Bond list overflow, boost fix_mscg max
A site has more bond/angle/dihedral partners that the maximum and
has overflowed the bond/angle/dihedral partners list. Increase the
corresponding fix_mscg max arg.
UNDOCUMENTED
E: Angle list overflow, boost fix_mscg max
UNDOCUMENTED
E: Dihedral list overflow, boost fix_mscg max
UNDOCUMENTED
W: Fix mscg n_frames is inconsistent with control.in
@ -87,4 +97,14 @@ that should be a divisor of the number of frames processed by the
fix mscg command. If not, the fix will still run, but some frames may
not be included in the MSCG calculations.
U: Fix mscg does not yet support mpi
Self-explanatory.
U: Bond/Angle/Dihedral list overflow, boost fix_mscg max
A site has more bond/angle/dihedral partners that the maximum and
has overflowed the bond/angle/dihedral partners list. Increase the
corresponding fix_mscg max arg.
*/

12
src/PYTHON/fix_python_invoke.h
View File

@ -51,4 +51,16 @@ 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: Unsupported callback name for fix python/invoke
UNDOCUMENTED
E: Could not initialize embedded Python
UNDOCUMENTED
E: Could not find Python function
UNDOCUMENTED
*/

42
src/PYTHON/fix_python_move.h
View File

@ -58,7 +58,47 @@ class FixPythonMove : public Fix {
/* ERROR/WARNING messages:
E: Illegal ... command
E: Fix python/integrate requires fully qualified class name
UNDOCUMENTED
E: Loading python integrator module failure
UNDOCUMENTED
E: Could not find integrator class in module'
UNDOCUMENTED
E: Could not instantiate instance of integrator class'
UNDOCUMENTED
E: Could not find 'init' method'
UNDOCUMENTED
E: Could not find 'initial_integrate' method'
UNDOCUMENTED
E: Could not find 'final_integrate' method'
UNDOCUMENTED
E: Could not find 'initial_integrate_respa' method'
UNDOCUMENTED
E: Could not find 'final_integrate_respa' method'
UNDOCUMENTED
E: Could not find 'reset_dt' method'
UNDOCUMENTED
U: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a

78
src/PYTHON/pair_python.h
View File

@ -59,6 +59,30 @@ class PairPython : public Pair {
/* ERROR/WARNING messages:
E: Could not find 'compute_force' method'
UNDOCUMENTED
E: Python 'compute_force' is not callable
UNDOCUMENTED
E: Could not find 'compute_energy' method'
UNDOCUMENTED
E: Python 'compute_energy' is not callable
UNDOCUMENTED
E: Could not create tuple for 'compute' function arguments
UNDOCUMENTED
E: Calling 'compute_force' function failed
UNDOCUMENTED
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
@ -69,7 +93,59 @@ E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair cutoff < Respa interior cutoff
E: Python pair style requires fully qualified class name
UNDOCUMENTED
E: Loading python pair style module failure
UNDOCUMENTED
E: Could not find pair style class in module'
UNDOCUMENTED
E: Could not instantiate instance of pair style class'
UNDOCUMENTED
E: Could not find 'check_units' method'
UNDOCUMENTED
E: Python 'check_units' is not callable
UNDOCUMENTED
E: Could not create tuple for 'check_units' function arguments
UNDOCUMENTED
E: Calling 'check_units' function failed
UNDOCUMENTED
E: Could not find 'map_coeff' method'
UNDOCUMENTED
E: Python 'map_coeff' is not callable
UNDOCUMENTED
E: Could not create tuple for 'map_coeff' function arguments
UNDOCUMENTED
E: Calling 'map_coeff' function failed
UNDOCUMENTED
E: Calling 'compute_energy' function failed
UNDOCUMENTED
U: Pair cutoff < Respa interior cutoff
One or more pairwise cutoffs are too short to use with the specified
rRESPA cutoffs.

26
src/PYTHON/python_impl.h
View File

@ -65,6 +65,10 @@ class PythonImpl : protected Pointers, public PythonInterface {
/* ERROR/WARNING messages:
E: Could not initialize embedded Python
The main module in Python was not accessible.
E: Invalid python command
Self-explanatory. Check the input script syntax and compare to the
@ -80,14 +84,9 @@ E: Python variable does not match Python function
This matching is defined by the python-style variable and the python
command.
E: Cannot embed Python when also extending Python with LAMMPS
E: Could not process Python source command
When running LAMMPS via Python through the LAMMPS library interface
you cannot also user the input script python command.
E: Could not initialize embedded Python
The main module in Python was not accessible.
UNDOCUMENTED
E: Could not open Python file
@ -123,10 +122,23 @@ E: Could not evaluate Python function input variable
Self-explanatory.
E: Unsupported variable type
UNDOCUMENTED
E: Python function evaluation failed
The Python function did not run successfully and/or did not return a
value (if it is supposed to return a value). This is probably due to
some error condition in the function.
E: Python command length keyword cannot be used unless output is a string
UNDOCUMENTED
U: Cannot embed Python when also extending Python with LAMMPS
When running LAMMPS via Python through the LAMMPS library interface
you cannot also user the input script python command.
*/

2
src/Purge.list
View File

@ -16,6 +16,8 @@ style_region.h
style_neigh_bin.h
style_neigh_pair.h
style_neigh_stencil.h
# deleted on 4 April 2018
pair_kim_version.h
# deleted on 15 December 2017
fix_python.cpp
fix_python.h

4
src/REAX/fix_reax_bonds.h
View File

@ -56,6 +56,10 @@ 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: Cannot open gzipped file
UNDOCUMENTED
E: Cannot open fix reax/bonds file %s
The output file for the fix reax/bonds command cannot be opened.

8
src/REAX/pair_reax.h
View File

@ -97,9 +97,9 @@ class PairREAX : public Pair {
/* ERROR/WARNING messages:
W: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c
W: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead
Self-explanatory.
UNDOCUMENTED
E: Reax_defs.h setting for NATDEF is too small
@ -147,4 +147,8 @@ E: Invalid REAX atom type
There is a mis-match between LAMMPS atom types and the elements
listed in the ReaxFF force field file.
U: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c
Self-explanatory.
*/

10
src/REPLICA/fix_neb.h
View File

@ -89,7 +89,15 @@ E: Potential energy ID for fix neb does not exist
Self-explanatory.
E: Atom count changed in fix neb
E: Too many active NEB atoms
UNDOCUMENTED
E: Too many atoms for NEB
UNDOCUMENTED
U: Atom count changed in fix neb
This is not allowed in a NEB calculation.

16
src/REPLICA/neb.h
View File

@ -82,14 +82,6 @@ E: Cannot use NEB with a single replica
Self-explanatory.
E: Can only use NEB with 1-processor replicas
This is current restriction for NEB as implemented in LAMMPS.
E: Cannot use NEB with atom_modify sort enabled
This is current restriction for NEB implemented in LAMMPS.
E: Cannot use NEB unless atom map exists
Use the atom_modify command to create an atom map.
@ -134,4 +126,12 @@ The specified file cannot be opened. Check that the path and name are
correct. If the file is a compressed file, also check that the gzip
executable can be found and run.
U: Can only use NEB with 1-processor replicas
This is current restriction for NEB as implemented in LAMMPS.
U: Cannot use NEB with atom_modify sort enabled
This is current restriction for NEB implemented in LAMMPS.
*/

10
src/REPLICA/prd.h
View File

@ -136,14 +136,14 @@ E: Cannot use PRD with a time-dependent region defined
PRD alters the timestep in ways that will mess up these regions.
E: Cannot use PRD with atom_modify sort enabled
This is a current restriction of PRD. You must turn off sorting,
which is enabled by default, via the atom_modify command.
E: Too many iterations
You must use a number of iterations that fit in a 32-bit integer
for minimization.
U: Cannot use PRD with atom_modify sort enabled
This is a current restriction of PRD. You must turn off sorting,
which is enabled by default, via the atom_modify command.
*/

14
src/REPLICA/temper.h
View File

@ -80,6 +80,10 @@ E: Tempering fix ID is not defined
The fix ID specified by the temper command does not exist.
E: Illegal temperature index
UNDOCUMENTED
E: Invalid frequency in temper command
Nevery must be > 0.
@ -89,10 +93,9 @@ E: Non integer # of swaps in temper command
Swap frequency in temper command must evenly divide the total # of
timesteps.
E: Tempering temperature fix is not valid
E: Tempering temperature fix is not supported
The fix specified by the temper command is not one that controls
temperature (nvt or langevin).
UNDOCUMENTED
E: Too many timesteps
@ -103,4 +106,9 @@ E: Tempering could not find thermo_pe compute
This compute is created by the thermo command. It must have been
explicitly deleted by a uncompute command.
U: Tempering temperature fix is not valid
The fix specified by the temper command is not one that controls
temperature (nvt or langevin).
*/

18
src/RIGID/compute_rigid_local.h
View File

@ -61,15 +61,27 @@ 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: Compute bond/local used when bonds are not allowed
E: Invalid keyword in compute rigid/local command
UNDOCUMENTED
E: FixRigidSmall ID for compute rigid/local does not exist
UNDOCUMENTED
E: Compute rigid/local does not use fix rigid/small fix
UNDOCUMENTED
U: Compute bond/local used when bonds are not allowed
The atom style does not support bonds.
E: Invalid keyword in compute bond/local command
U: Invalid keyword in compute bond/local command
Self-explanatory.
E: No bond style is defined for compute bond/local
U: No bond style is defined for compute bond/local
Self-explanatory.

60
src/RIGID/fix_ehex.h
View File

@ -75,27 +75,25 @@ class FixEHEX : public Fix {
/* ERROR/WARNING messages:
E: Illegal fix ehex command: wrong number of parameters
E: Illegal fix ehex command: wrong number of parameters
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.
UNDOCUMENTED
E: Illegal fix ehex command: integer value expected
E: Illegal ... command
Self-explanatory. Check the value for nevery.
UNDOCUMENTED
E: Region ID for fix ehex does not exist
Self-explanatory.
E: You can only use the keyword 'com' together with the keyword 'constrain' .
E: Illegal fix ehex keyword
Self-explanatory.
UNDOCUMENTED
E: Illegal fix ehex keyword
E: You can only use the keyword 'com' together with the keyword 'constrain'
Self-explanatory.
UNDOCUMENTED
E: Fix ehex group has no atoms
@ -109,22 +107,48 @@ E: Fix ehex was configured with keyword constrain, but shake/rattle was not defi
The option constrain requires either fix shake or fix rattle which is missing in the input script.
E: Fix heat kinetic energy went negative
E: Fix ehex kinetic energy went negative
This will cause the velocity rescaling about to be performed by fix
heat to be invalid.
E: Fix heat kinetic energy of an atom went negative
This will cause the velocity rescaling about to be performed by fix
heat to be invalid.
UNDOCUMENTED
E: Internal error: shake_flag[m] has to be between 1 and 4 for m in nlist
Contact developers.
E: Fix ehex shake cluster has almost zero mass.
UNDOCUMENTED
E: Fix ehex error mass of region is close to zero
Check your configuration.
U: Illegal fix ehex command: wrong number of parameters
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.
U: Illegal fix ehex command: integer value expected
Self-explanatory. Check the value for nevery.
U: You can only use the keyword 'com' together with the keyword 'constrain' .
Self-explanatory.
U: Illegal fix ehex keyword
Self-explanatory.
U: Fix heat kinetic energy went negative
This will cause the velocity rescaling about to be performed by fix
heat to be invalid.
U: Fix heat kinetic energy of an atom went negative
This will cause the velocity rescaling about to be performed by fix
heat to be invalid.
*/

37
src/RIGID/fix_rattle.h
View File

@ -77,30 +77,49 @@ class FixRattle : public FixShake {
#endif
#endif
/* ERROR/WARNING messages:
W: Fix rattle should come after all other integration fixes
W: Fix rattle should come after all other integration fixes
This fix is designed to work after all other integration fixes change
atom positions. Thus it should be the last integration fix specified.
If not, it will not satisfy the desired constraints as well as it
otherwise would.
UNDOCUMENTED
E: Rattle determinant = 0.0
The determinant of the matrix being solved for a single cluster
specified by the fix rattle command is numerically invalid.
E: Rattle failed
E: Rattle failed
UNDOCUMENTED
E: Coordinate constraints are not satisfied up to desired tolerance
UNDOCUMENTED
E: Velocity constraints are not satisfied up to desired tolerance
UNDOCUMENTED
E: Velocity constraints are not satisfied up to desired tolerance!
UNDOCUMENTED
U: Fix rattle should come after all other integration fixes
This fix is designed to work after all other integration fixes change
atom positions. Thus it should be the last integration fix specified.
If not, it will not satisfy the desired constraints as well as it
otherwise would.
U: Rattle failed
Certain constraints were not satisfied.
E: Coordinate constraints are not satisfied up to desired tolerance
U: Coordinate constraints are not satisfied up to desired tolerance
Self-explanatory.
E: Rattle velocity constraints are not satisfied up to desired tolerance
U: Rattle velocity constraints are not satisfied up to desired tolerance
Self-explanatory.

20
src/RIGID/fix_rigid.h
View File

@ -161,6 +161,26 @@ Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Fix rigid custom requires previously defined property/atom
UNDOCUMENTED
E: Fix rigid custom requires integer-valued property/atom
UNDOCUMENTED
E: Variable name for fix rigid custom does not exist
UNDOCUMENTED
E: Fix rigid custom variable is no atom-style variable
UNDOCUMENTED
E: Unsupported fix rigid custom property
UNDOCUMENTED
E: Fix rigid molecule requires atom attribute molecule
Self-explanatory.

20
src/RIGID/fix_rigid_small.h
View File

@ -223,6 +223,26 @@ E: Fix rigid/small requires atom attribute molecule
Self-explanatory.
E: Fix rigid/small custom requires previously defined property/atom
UNDOCUMENTED
E: Fix rigid/small custom requires integer-valued property/atom
UNDOCUMENTED
E: Variable name for fix rigid/small custom does not exist
UNDOCUMENTED
E: Fix rigid/small custom variable is no atom-style variable
UNDOCUMENTED
E: Unsupported fix rigid custom property
UNDOCUMENTED
E: Fix rigid/small requires an atom map, see atom_modify
Self-explanatory.

4
src/SHOCK/fix_msst.h
View File

@ -149,6 +149,10 @@ E: Fix msst compute ID does not compute potential energy
Self-explanatory.
E: Fix msst dftb cannot be used w/out fix external
UNDOCUMENTED
E: Could not find fix_modify temperature ID
The compute ID for computing temperature does not exist.

8
src/SNAP/compute_snad_atom.h
View File

@ -66,12 +66,16 @@ E: Compute snad/atom requires a pair style be defined
Self-explanatory.
E: Compute snad/atom cutoff is longer than pairwise cutoff
E: Compute sna/atom cutoff is longer than pairwise cutoff
Self-explanatory.
UNDOCUMENTED
W: More than one compute snad/atom
Self-explanatory.
U: Compute snad/atom cutoff is longer than pairwise cutoff
Self-explanatory.
*/

4
src/SNAP/pair_snap.h
View File

@ -137,6 +137,10 @@ E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Incorrect SNAP coeff file
UNDOCUMENTED
E: Incorrect SNAP parameter file
The file cannot be parsed correctly, check its internal syntax.

45
src/USER-MISC/fix_ave_correlate_long.cpp
View File

@ -31,6 +31,7 @@
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
#include "force.h"
@ -45,11 +46,24 @@ enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL};
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
static const char cite_fix_ave_correlate_long[] =
"fix ave/correlate/long command:\n\n"
"@Article{Ramirez10,\n"
" author = {Jorge Rami{\'}rez and Sathish K. Sukumaran and Bart Vorselaars and Alexei E. Likhtman},\n"
" title = {Efficient on the fly calculation of time correlation functions in computer simulations},"
" journal = {J.~Chem.~Phys.},\n"
" year = 2010,\n"
" volume = 133,\n"
" pages = {154103}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
Fix (lmp, narg, arg)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_ave_correlate_long);
// At least nevery nfrez and one value are needed
if (narg < 6) error->all(FLERR,"Illegal fix ave/correlate/long command");
@ -321,6 +335,8 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
nvalid_last = -1;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
last_accumulated_step = -1;
}
/* ---------------------------------------------------------------------- */
@ -479,7 +495,7 @@ void FixAveCorrelateLong::end_of_step()
fprintf(fp,"# Timestep: " BIGINT_FORMAT "\n", ntimestep);
for (unsigned int i=0;i<npcorr;++i) {
fprintf(fp, "%lg ", t[i]*update->dt);
for (unsigned int j=0;j<npair;++j) {
for (int j=0;j<npair;++j) {
fprintf(fp, "%lg ", f[j][i]);
}
fprintf(fp, "\n");
@ -499,7 +515,7 @@ void FixAveCorrelateLong::evaluate() {
unsigned int jm=0;
// First correlator
for (unsigned int j=0;j<p;++j) {
for (int j=0;j<p;++j) {
if (ncorrelation[0][j] > 0) {
t[jm] = j;
for (int i=0;i<npair;++i)
@ -532,7 +548,7 @@ void FixAveCorrelateLong::accumulate()
{
int i,j,ipair;
//printf("DEBUG %i %i\n", nvalues, npair);
if (update->ntimestep <= last_accumulated_step) return;
if (type == AUTO) {
for (i=0; i<nvalues;i++) add(i,values[i]);
@ -566,13 +582,14 @@ void FixAveCorrelateLong::accumulate()
else add(ipair++,values[i],values[j]);
}
}
last_accumulated_step = update->ntimestep;
}
/* ----------------------------------------------------------------------
Add a scalar value to the autocorrelator k of pair i
------------------------------------------------------------------------- */
void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k){
void FixAveCorrelateLong::add(const int i, const double w, const int k){
// If we exceed the correlator side, the value is discarded
if (k == numcorrelators) return;
if (k > kmax) kmax=k;
@ -593,7 +610,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k)
unsigned int ind1=insertindex[k];
if (k==0) { // First correlator is different
int ind2=ind1;
for (unsigned int j=0;j<p;++j) {
for (int j=0;j<p;++j) {
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
if (i==0) ++ncorrelation[k][j];
@ -603,7 +620,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k)
}
} else {
int ind2=ind1-dmin;
for (unsigned int j=dmin;j<p;++j) {
for (int j=dmin;j<p;++j) {
if (ind2<0) ind2+=p;
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
@ -624,7 +641,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k)
Add 2 scalar values to the cross-correlator k of pair i
------------------------------------------------------------------------- */
void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
const unsigned int k) {
const int k) {
if (k == numcorrelators) return;
if (k > kmax) kmax=k;
@ -644,7 +661,7 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
unsigned int ind1=insertindex[k];
if (k==0) {
int ind2=ind1;
for (unsigned int j=0;j<p;++j) {
for (int j=0;j<p;++j) {
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
if (i==0) ++ncorrelation[k][j];
@ -655,7 +672,7 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
}
else {
int ind2=ind1-dmin;
for (unsigned int j=dmin;j<p;++j) {
for (int j=dmin;j<p;++j) {
if (ind2<0) ind2+=p;
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
@ -699,8 +716,8 @@ double FixAveCorrelateLong::memory_usage() {
// ncorrelation: numcorrelators x p
// naccumulator: numcorrelators
// insertindex: numcorrelators
// t: numcorrelators x p
// f: npair x numcorrelators x p
// t: numcorrelators x p
// f: npair x numcorrelators x p
double bytes = (4*npair*numcorrelators*p + 2*npair*numcorrelators
+ numcorrelators*p)*sizeof(double)
+ numcorrelators*p*sizeof(unsigned long int)
@ -723,8 +740,7 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
list[n++]=numcorrelators;
list[n++]=p;
list[n++]=m;
list[n++]=nvalid;
list[n++]=nvalid_last;
list[n++] = last_accumulated_step;
for (int i=0;i<npair;i++)
for (int j=0;j<numcorrelators;j++) {
for (int k=0;k<p;k++) {
@ -760,8 +776,7 @@ void FixAveCorrelateLong::restart(char *buf)
int numcorrelatorsin = static_cast<int> (list[n++]);
int pin = static_cast<int> (list[n++]);
int min = static_cast<int> (list[n++]);
nvalid = static_cast<int> (list[n++]);
nvalid_last = static_cast<int> (list[n++]);
last_accumulated_step = static_cast<int> (list[n++]);
if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators)
|| (pin!=p) || (min!=m))

14
src/USER-MISC/fix_ave_correlate_long.h
View File

@ -51,17 +51,17 @@ class FixAveCorrelateLong : public Fix {
unsigned int *naccumulator;
unsigned int *insertindex;
unsigned int numcorrelators; // Recommended 20
unsigned int p; // Points per correlator (recommended 16)
int numcorrelators; // Recommended 20
int p; // Points per correlator (recommended 16)
unsigned int m; // Num points for average (recommended 2; p mod m = 0)
unsigned int dmin; // Min distance between ponts for correlators k>0; dmin=p/m
unsigned int length; // Length of result arrays
unsigned int kmax; // Maximum correlator attained during simulation
int length; // Length of result arrays
int kmax; // Maximum correlator attained during simulation
int me,nvalues;
int nfreq;
bigint nvalid,nvalid_last;
bigint nvalid,nvalid_last,last_accumulated_step;
int *which,*argindex,*value2index;
char **ids;
FILE *fp;
@ -76,8 +76,8 @@ class FixAveCorrelateLong : public Fix {
void evaluate();
bigint nextvalid();
void add(const int i, const double w, const unsigned int k = 0);
void add(const int i, const double wA, const double wB, const unsigned int k = 0);
void add(const int i, const double w, const int k = 0);
void add(const int i, const double wA, const double wB, const int k = 0);
};

8
src/VORONOI/compute_voronoi_atom.h
View File

@ -82,6 +82,14 @@ E: Illegal compute voronoi/atom command (occupation and (surface or edges))
Self-explanatory.
E: Compute voronoi/atom occupation requires an atom map, see atom_modify
UNDOCUMENTED
E: Compute voronoi/atom occupation requires atom IDs
UNDOCUMENTED
E: Variable name for voronoi radius does not exist
Self-explanatory.

4
src/angle_zero.h
View File

@ -54,6 +54,10 @@ class AngleZero : public Angle {
/* ERROR/WARNING messages:
E: Illegal ... command
UNDOCUMENTED
E: Incorrect args for angle coefficients
Self-explanatory. Check the input script or data file.

50
src/atom.h
View File

@ -478,31 +478,6 @@ E: Invalid atom ID in Bodies section of data file
Atom IDs must be positive integers and within range of defined
atoms.
E: Cannot set mass for this atom style
This atom style does not support mass settings for each atom type.
Instead they are defined on a per-atom basis in the data file.
E: Invalid mass line in data file
Self-explanatory.
E: Invalid type for mass set
Mass command must set a type from 1-N where N is the number of atom
types.
E: Invalid mass value
Self-explanatory.
E: All masses are not set
For atom styles that define masses for each atom type, all masses must
be set in the data file or by the mass command before running a
simulation. They must also be set before using the velocity
command.
E: Reuse of molecule template ID
The template IDs must be unique.
@ -523,4 +498,29 @@ E: Too many atom sorting bins
This is likely due to an immense simulation box that has blown up
to a large size.
U: Cannot set mass for this atom style
This atom style does not support mass settings for each atom type.
Instead they are defined on a per-atom basis in the data file.
U: Invalid mass line in data file
Self-explanatory.
U: Invalid type for mass set
Mass command must set a type from 1-N where N is the number of atom
types.
U: Invalid mass value
Self-explanatory.
U: All masses are not set
For atom styles that define masses for each atom type, all masses must
be set in the data file or by the mass command before running a
simulation. They must also be set before using the velocity
command.
*/

20
src/atom_map.h Normal file
View File

@ -0,0 +1,20 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ERROR/WARNING messages:
E: Cannot create an atom map unless atoms have IDs
UNDOCUMENTED
*/

16
src/balance.h
View File

@ -109,10 +109,6 @@ 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: Cannot open balance output file
Self-explanatory.
E: Cannot balance in z dimension for 2d simulation
Self-explanatory.
@ -129,10 +125,22 @@ E: Lost atoms via balance: original %ld current %ld
This should not occur. Report the problem to the developers.
E: Unknown (fix) balance weight method
UNDOCUMENTED
E: Cannot open (fix) balance output file
UNDOCUMENTED
E: Balance produced bad splits
This should not occur. It means two or more cutting plane locations
are on top of each other or out of order. Report the problem to the
developers.
U: Cannot open balance output file
Self-explanatory.
*/

20
src/bond.h
View File

@ -84,4 +84,24 @@ E: All bond coeffs are not set
All bond coefficients must be set in the data file or by the
bond_coeff command before running a simulation.
E: Illegal ... command
UNDOCUMENTED
E: Invalid atom types in bond_write command
UNDOCUMENTED
E: Invalid rlo/rhi values in bond_write command
UNDOCUMENTED
E: Cannot open bond_write file
UNDOCUMENTED
E: Fix adapt interface to this bond style not supported
UNDOCUMENTED
*/

4
src/bond_zero.h
View File

@ -54,6 +54,10 @@ class BondZero : public Bond {
/* ERROR/WARNING messages:
E: Illegal ... command
UNDOCUMENTED
E: Incorrect args for bond coefficients
Self-explanatory. Check the input script or data file.

4
src/change_box.h
View File

@ -117,6 +117,10 @@ This is because those fixes store the shape of the box. You need to
use unfix to discard the fix, change the box, then redefine a new
fix.
W: Attempting to remap atoms in rigid bodies
UNDOCUMENTED
W: Lost atoms via change_box: original %ld current %ld
The command options you have used caused atoms to be lost.

14
src/comm.h
View File

@ -145,11 +145,6 @@ class Comm : protected Pointers {
/* ERROR/WARNING messages:
W: OMP_NUM_THREADS environment is not set.
This environment variable must be set appropriately to use the
USER-OMP package.
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
@ -220,4 +215,13 @@ E: Processor count in z must be 1 for 2d simulation
Self-explanatory.
E: Cannot put data on ring from NULL pointer
UNDOCUMENTED
U: OMP_NUM_THREADS environment is not set.
This environment variable must be set appropriately to use the
USER-OMP package.
*/

Some files were not shown because too many files have changed in this diff Show More