Merge branch 'master' into USER-DPD_kokkos_testing
This commit is contained in:
Stan Moore
Binary file not shown.
|
Before Width: | Height: | Size: 14 KiB After Width: | Height: | Size: 14 KiB |
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="19 May 2017 version">
|
||||
<META NAME="docnumber" CONTENT="23 Jun 2017 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>
|
||||
@ -21,7 +21,7 @@
|
||||
<H1></H1>
|
||||
|
||||
LAMMPS Documentation :c,h3
|
||||
19 May 2017 version :c,h4
|
||||
23 Jun 2017 version :c,h4
|
||||
|
||||
Version info: :h4
|
||||
|
||||
|
||||
@ -964,7 +964,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
"lj/expand (gko)"_pair_lj_expand.html,
|
||||
"lj/gromacs (gko)"_pair_gromacs.html,
|
||||
"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
|
||||
"lj/long/coul/long (o)"_pair_lj_long.html,
|
||||
"lj/long/coul/long (io)"_pair_lj_long.html,
|
||||
"lj/long/dipole/long"_pair_dipole.html,
|
||||
"lj/long/tip4p/long"_pair_lj_long.html,
|
||||
"lj/smooth (o)"_pair_lj_smooth.html,
|
||||
@ -1073,7 +1073,7 @@ package"_Section_start.html#start_3.
|
||||
"table/rx"_pair_table_rx.html,
|
||||
"tersoff/table (o)"_pair_tersoff.html,
|
||||
"thole"_pair_thole.html,
|
||||
"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
|
||||
"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
|
||||
|
||||
:line
|
||||
|
||||
@ -1225,7 +1225,7 @@ USER-OMP, t = OPT.
|
||||
"msm/cg (o)"_kspace_style.html,
|
||||
"pppm (go)"_kspace_style.html,
|
||||
"pppm/cg (o)"_kspace_style.html,
|
||||
"pppm/disp"_kspace_style.html,
|
||||
"pppm/disp (i)"_kspace_style.html,
|
||||
"pppm/disp/tip4p"_kspace_style.html,
|
||||
"pppm/stagger"_kspace_style.html,
|
||||
"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
|
||||
|
||||
@ -1938,7 +1938,7 @@ documentation in the src/library.cpp file for details, including
|
||||
which quantities can be queried by name:
|
||||
|
||||
void *lammps_extract_global(void *, char *)
|
||||
void lammps_extract_box(void *, double *, double *,
|
||||
void lammps_extract_box(void *, double *, double *,
|
||||
double *, double *, double *, int *, int *)
|
||||
void *lammps_extract_atom(void *, char *)
|
||||
void *lammps_extract_compute(void *, char *, int, int)
|
||||
@ -2682,14 +2682,14 @@ bond_coeff 2 25.724 0.0 :pre
|
||||
|
||||
When running dynamics with the adiabatic core/shell model, the
|
||||
following issues should be considered. The relative motion of
|
||||
the core and shell particles corresponds to the polarization,
|
||||
hereby an instantaneous relaxation of the shells is approximated
|
||||
the core and shell particles corresponds to the polarization,
|
||||
hereby an instantaneous relaxation of the shells is approximated
|
||||
and a fast core/shell spring frequency ensures a nearly constant
|
||||
internal kinetic energy during the simulation.
|
||||
internal kinetic energy during the simulation.
|
||||
Thermostats can alter this polarization behaviour, by scaling the
|
||||
internal kinetic energy, meaning the shell will not react freely to
|
||||
its electrostatic environment.
|
||||
Therefore it is typically desirable to decouple the relative motion of
|
||||
internal kinetic energy, meaning the shell will not react freely to
|
||||
its electrostatic environment.
|
||||
Therefore it is typically desirable to decouple the relative motion of
|
||||
the core/shell pair, which is an imaginary degree of freedom, from the
|
||||
real physical system. To do that, the "compute
|
||||
temp/cs"_compute_temp_cs.html command can be used, in conjunction with
|
||||
@ -2721,13 +2721,13 @@ fix thermostatequ all nve # integrator as needed f
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
|
||||
|
||||
The pressure for the core/shell system is computed via the regular
|
||||
LAMMPS convention by "treating the cores and shells as individual
|
||||
particles"_#MitchellFincham2. For the thermo output of the pressure
|
||||
as well as for the application of a barostat, it is necessary to
|
||||
use an additional "pressure"_compute_pressure compute based on the
|
||||
default "temperature"_compute_temp and specifying it as a second
|
||||
argument in "fix modify"_fix_modify.html and
|
||||
The pressure for the core/shell system is computed via the regular
|
||||
LAMMPS convention by "treating the cores and shells as individual
|
||||
particles"_#MitchellFincham2. For the thermo output of the pressure
|
||||
as well as for the application of a barostat, it is necessary to
|
||||
use an additional "pressure"_compute_pressure compute based on the
|
||||
default "temperature"_compute_temp and specifying it as a second
|
||||
argument in "fix modify"_fix_modify.html and
|
||||
"thermo_modify"_thermo_modify.html resulting in:
|
||||
|
||||
(...)
|
||||
@ -2757,18 +2757,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
|
||||
velocity all create 1427 134 bias yes temp CSequ
|
||||
velocity all scale 1427 temp CSequ :pre
|
||||
|
||||
To maintain the correct polarizability of the core/shell pairs, the
|
||||
kinetic energy of the internal motion shall remain nearly constant.
|
||||
Therefore the choice of spring force and mass ratio need to ensure
|
||||
much faster relative motion of the 2 atoms within the core/shell pair
|
||||
than their center-of-mass velocity. This allows the shells to
|
||||
effectively react instantaneously to the electrostatic environment and
|
||||
To maintain the correct polarizability of the core/shell pairs, the
|
||||
kinetic energy of the internal motion shall remain nearly constant.
|
||||
Therefore the choice of spring force and mass ratio need to ensure
|
||||
much faster relative motion of the 2 atoms within the core/shell pair
|
||||
than their center-of-mass velocity. This allows the shells to
|
||||
effectively react instantaneously to the electrostatic environment and
|
||||
limits energy transfer to or from the core/shell oscillators.
|
||||
This fast movement also dictates the timestep that can be used.
|
||||
|
||||
The primary literature of the adiabatic core/shell model suggests that
|
||||
the fast relative motion of the core/shell pairs only allows negligible
|
||||
energy transfer to the environment.
|
||||
energy transfer to the environment.
|
||||
The mentioned energy transfer will typically lead to a small drift
|
||||
in total energy over time. This internal energy can be monitored
|
||||
using the "compute chunk/atom"_compute_chunk_atom.html and "compute
|
||||
@ -2790,7 +2790,7 @@ pairs as chunks.
|
||||
|
||||
For example if core/shell pairs are the only molecules:
|
||||
|
||||
read_data NaCl_CS_x0.1_prop.data
|
||||
read_data NaCl_CS_x0.1_prop.data
|
||||
compute prop all property/atom molecule
|
||||
compute cs_chunk all chunk/atom c_prop
|
||||
compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
|
||||
|
||||
@ -585,7 +585,7 @@ do not recommend building with other acceleration packages installed
|
||||
|
||||
make yes-kokkos
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-kokkos
|
||||
make machine :pre
|
||||
|
||||
@ -839,13 +839,13 @@ written and read in parallel.
|
||||
Note that MPIIO is part of the standard message-passing interface
|
||||
(MPI) library, so you should not need any additional compiler or link
|
||||
settings, beyond what LAMMPS normally uses for MPI on your system.
|
||||
|
||||
|
||||
make yes-mpiio
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-mpiio
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/MPIIO: filenames -> commands
|
||||
@ -855,7 +855,7 @@ src/MPIIO: filenames -> commands
|
||||
"read_restart"_read_restart.html :ul
|
||||
|
||||
:line
|
||||
|
||||
|
||||
MSCG package :link(mscg),h4
|
||||
|
||||
[Contents:]
|
||||
@ -914,7 +914,7 @@ lib/mscg/README
|
||||
examples/mscg :ul
|
||||
|
||||
:line
|
||||
|
||||
|
||||
OPT package :link(OPT),h4
|
||||
|
||||
[Contents:]
|
||||
@ -1387,7 +1387,7 @@ atomic information to continuum fields.
|
||||
[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
Before building LAMMPS with this package, you must first build the ATC
|
||||
library in lib/atc. You can do this manually if you prefer; follow
|
||||
the instructions in lib/atc/README. You can also do it in one step
|
||||
@ -1420,10 +1420,10 @@ usual manner:
|
||||
|
||||
make yes-user-atc
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-atc
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-ATC: filenames -> commands
|
||||
@ -1446,7 +1446,7 @@ model.
|
||||
[Author:] Ilya Valuev (JIHT, Russia).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
Before building LAMMPS with this package, you must first build the
|
||||
AWPMD library in lib/awpmd. You can do this manually if you prefer;
|
||||
follow the instructions in lib/awpmd/README. You can also do it in
|
||||
@ -1479,10 +1479,10 @@ usual manner:
|
||||
|
||||
make yes-user-awpmd
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-awpmd
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-AWPMD: filenames -> commands
|
||||
@ -1505,13 +1505,13 @@ stability.
|
||||
[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-cgdna
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-cgdna
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-CGDNA: filenames -> commands
|
||||
@ -1536,13 +1536,13 @@ acids.
|
||||
[Author:] Axel Kohlmeyer (Temple U).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-cgsdk
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-cgsdk
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-CGSDK: filenames -> commands
|
||||
@ -1570,7 +1570,7 @@ by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
|
||||
Jerome Henin (LISM, CNRS, Marseille, France).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
Before building LAMMPS with this package, you must first build the
|
||||
COLVARS library in lib/colvars. You can do this manually if you
|
||||
prefer; follow the instructions in lib/colvars/README. You can also
|
||||
@ -1594,10 +1594,10 @@ usual manner:
|
||||
|
||||
make yes-user-colvars
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-colvars
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-COLVARS: filenames -> commands
|
||||
@ -1619,13 +1619,13 @@ intensities based on kinematic diffraction theory.
|
||||
[Author:] Shawn Coleman while at the U Arkansas.
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-diffraction
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-diffraction
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-DIFFRACTION: filenames -> commands
|
||||
@ -1654,13 +1654,13 @@ algorithm.
|
||||
Brennan (ARL).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-dpd
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-dpd
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-DPD: filenames -> commands
|
||||
@ -1696,13 +1696,13 @@ tools/drude.
|
||||
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-drude
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-drude
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-DRUDE: filenames -> commands
|
||||
@ -1734,13 +1734,13 @@ tools/eff; see its README file.
|
||||
[Author:] Andres Jaramillo-Botero (CalTech).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-eff
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-eff
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-EFF: filenames -> commands
|
||||
@ -1773,13 +1773,13 @@ for using this package in tools/fep; see its README file.
|
||||
[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-fep
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-fep
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-FEP: filenames -> commands
|
||||
@ -1836,13 +1836,13 @@ file.
|
||||
|
||||
You can then install/un-install the package and build LAMMPS in the
|
||||
usual manner:
|
||||
|
||||
|
||||
make yes-user-h5md
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-h5md
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-H5MD: filenames -> commands
|
||||
@ -1908,7 +1908,7 @@ explained in "Section 5.3.2"_accelerate_intel.html.
|
||||
|
||||
make yes-user-intel yes-user-omp
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-intel no-user-omp
|
||||
make machine :pre
|
||||
|
||||
@ -1938,13 +1938,13 @@ can be used to model MD particles influenced by hydrodynamic forces.
|
||||
Ontario).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-lb
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-lb
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-LB: filenames -> commands
|
||||
@ -1972,13 +1972,13 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
|
||||
[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-mgpt
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-mgpt
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-MGPT: filenames -> commands
|
||||
@ -2000,13 +2000,13 @@ dihedral, improper, or command style.
|
||||
src/USER-MISC/README file.
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-misc
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-misc
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-MISC: filenames -> commands
|
||||
@ -2031,13 +2031,13 @@ n = grad(g).
|
||||
Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-manifold
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-manifold
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-MANIFOLD: filenames -> commands
|
||||
@ -2080,7 +2080,7 @@ at
|
||||
[Author:] Axel Kohlmeyer (Temple U).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
Note that the lib/molfile/Makefile.lammps file has a setting for a
|
||||
dynamic loading library libdl.a that should is typically present on
|
||||
all systems, which is required for LAMMPS to link with this package.
|
||||
@ -2090,10 +2090,10 @@ lib/molfile/Makefile.lammps for details.
|
||||
|
||||
make yes-user-molfile
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-molfile
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-MOLFILE: filenames -> commands
|
||||
@ -2128,7 +2128,7 @@ tools:
|
||||
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
Note that to follow these steps, you need the standard NetCDF software
|
||||
package installed on your system. The lib/netcdf/Makefile.lammps file
|
||||
has settings for NetCDF include and library files that LAMMPS needs to
|
||||
@ -2138,7 +2138,7 @@ lib/netcdf/README for details.
|
||||
|
||||
make yes-user-netcdf
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-netcdf
|
||||
make machine :pre
|
||||
|
||||
@ -2178,10 +2178,10 @@ Once you have an appropriate Makefile.machine, you can
|
||||
install/un-install the package and build LAMMPS in the usual manner:
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-omp
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-omp
|
||||
make machine :pre
|
||||
|
||||
@ -2213,13 +2213,13 @@ relations, directly from molecular dynamics simulations.
|
||||
[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-phonon
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-phonon
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-PHONON: filenames -> commands
|
||||
@ -2235,7 +2235,7 @@ USER-QMMM package :link(USER-QMMM),h4
|
||||
|
||||
A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
|
||||
QM/MM simulation, currently only in combination with the "Quantum
|
||||
ESPRESSO"_espresso package.
|
||||
ESPRESSO"_espresso package.
|
||||
|
||||
:link(espresso,http://www.quantum-espresso.org)
|
||||
|
||||
@ -2275,7 +2275,7 @@ usual manner:
|
||||
|
||||
make yes-user-qmmm
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-qmmm
|
||||
make machine :pre
|
||||
|
||||
@ -2284,7 +2284,7 @@ for a QM/MM simulation. You must also build Quantum ESPRESSO and
|
||||
create a new executable which links LAMMPS and Quanutm ESPRESSO
|
||||
together. These are steps 3 and 4 described in the lib/qmmm/README
|
||||
file.
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-QMMM: filenames -> commands
|
||||
@ -2312,13 +2312,13 @@ simulation.
|
||||
[Author:] Yuan Shen (Stanford U).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-qtb
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-qtb
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-QTB: filenames -> commands
|
||||
@ -2362,10 +2362,10 @@ usual manner:
|
||||
|
||||
make yes-user-quip
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-quip
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-QUIP: filenames -> commands
|
||||
@ -2388,13 +2388,13 @@ for monitoring molecules as bonds are created and destroyed.
|
||||
[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-reaxc
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-reaxc
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-REAXC: filenames -> commands
|
||||
@ -2451,10 +2451,10 @@ usual manner:
|
||||
|
||||
make yes-user-smd
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-smd
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-SMD: filenames -> commands
|
||||
@ -2477,13 +2477,13 @@ ionocovalent bonds in oxides.
|
||||
Tetot (LAAS-CNRS, France).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-smtbq
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-smtbq
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-SMTBQ: filenames -> commands
|
||||
@ -2516,13 +2516,13 @@ property/atom"_compute_property_atom.html command.
|
||||
Dynamics, Ernst Mach Institute, Germany).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-sph
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-sph
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-SPH: filenames -> commands
|
||||
@ -2544,13 +2544,13 @@ stress, etc) about individual interactions.
|
||||
[Author:] Axel Kohlmeyer (Temple U).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-tally
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-tally
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-TALLY: filenames -> commands
|
||||
@ -2577,7 +2577,7 @@ system.
|
||||
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
The lib/vtk/Makefile.lammps file has settings for accessing VTK files
|
||||
and its library, which are required for LAMMPS to build and link with
|
||||
this package. If the settings are not valid for your system, check if
|
||||
@ -2590,10 +2590,10 @@ usual manner:
|
||||
|
||||
make yes-user-vtk
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-vtk
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-VTK: filenames -> commands
|
||||
|
||||
@ -714,7 +714,7 @@ stored in the "image" property. All three image flags are stored in
|
||||
a packed format in a single integer, so count would be 1 to retrieve
|
||||
that integer, however also a count value of 3 can be used and then
|
||||
the image flags will be unpacked into 3 individual integers, ordered
|
||||
in a similar fashion as coordinates.
|
||||
in a similar fashion as coordinates.
|
||||
|
||||
Note that the data structure gather_atoms("x") returns is different
|
||||
from the data structure returned by extract_atom("x") in four ways.
|
||||
|
||||
@ -30,8 +30,8 @@ Dihedral Styles: charmm, harmonic, opls :l
|
||||
Fixes: nve, npt, nvt, nvt/sllod :l
|
||||
Improper Styles: cvff, harmonic :l
|
||||
Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
|
||||
charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
|
||||
K-Space Styles: pppm :l
|
||||
charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l
|
||||
K-Space Styles: pppm, pppm/disp :l
|
||||
:ule
|
||||
|
||||
[Speed-ups to expect:]
|
||||
@ -42,62 +42,88 @@ precision mode. Performance improvements are shown compared to
|
||||
LAMMPS {without using other acceleration packages} as these are
|
||||
under active development (and subject to performance changes). The
|
||||
measurements were performed using the input files available in
|
||||
the src/USER-INTEL/TEST directory. These are scalable in size; the
|
||||
results given are with 512K particles (524K for Liquid Crystal).
|
||||
Most of the simulations are standard LAMMPS benchmarks (indicated
|
||||
by the filename extension in parenthesis) with modifications to the
|
||||
run length and to add a warmup run (for use with offload
|
||||
benchmarks).
|
||||
the src/USER-INTEL/TEST directory with the provided run script.
|
||||
These are scalable in size; the results given are with 512K
|
||||
particles (524K for Liquid Crystal). Most of the simulations are
|
||||
standard LAMMPS benchmarks (indicated by the filename extension in
|
||||
parenthesis) with modifications to the run length and to add a
|
||||
warmup run (for use with offload benchmarks).
|
||||
|
||||
:c,image(JPG/user_intel.png)
|
||||
|
||||
Results are speedups obtained on Intel Xeon E5-2697v4 processors
|
||||
(code-named Broadwell) and Intel Xeon Phi 7250 processors
|
||||
(code-named Knights Landing) with "18 Jun 2016" LAMMPS built with
|
||||
Intel Parallel Studio 2016 update 3. Results are with 1 MPI task
|
||||
(code-named Knights Landing) with "June 2017" LAMMPS built with
|
||||
Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
|
||||
per physical core. See {src/USER-INTEL/TEST/README} for the raw
|
||||
simulation rates and instructions to reproduce.
|
||||
|
||||
:line
|
||||
|
||||
[Accuracy and order of operations:]
|
||||
|
||||
In most molecular dynamics software, parallelization parameters
|
||||
(# of MPI, OpenMP, and vectorization) can change the results due
|
||||
to changing the order of operations with finite-precision
|
||||
calculations. The USER-INTEL package is deterministic. This means
|
||||
that the results should be reproducible from run to run with the
|
||||
{same} parallel configurations and when using determinstic
|
||||
libraries or library settings (MPI, OpenMP, FFT). However, there
|
||||
are differences in the USER-INTEL package that can change the
|
||||
order of operations compared to LAMMPS without acceleration:
|
||||
|
||||
Neighbor lists can be created in a different order :ulb,l
|
||||
Bins used for sorting atoms can be oriented differently :l
|
||||
The default stencil order for PPPM is 7. By default, LAMMPS will
|
||||
calculate other PPPM parameters to fit the desired acuracy with
|
||||
this order :l
|
||||
The {newton} setting applies to all atoms, not just atoms shared
|
||||
between MPI tasks :l
|
||||
Vectorization can change the order for adding pairwise forces :l
|
||||
:ule
|
||||
|
||||
The precision mode (described below) used with the USER-INTEL
|
||||
package can change the {accuracy} of the calculations. For the
|
||||
default {mixed} precision option, calculations between pairs or
|
||||
triplets of atoms are performed in single precision, intended to
|
||||
be within the inherent error of MD simulations. All accumulation
|
||||
is performed in double precision to prevent the error from growing
|
||||
with the number of atoms in the simulation. {Single} precision
|
||||
mode should not be used without appropriate validation.
|
||||
|
||||
:line
|
||||
|
||||
[Quick Start for Experienced Users:]
|
||||
|
||||
LAMMPS should be built with the USER-INTEL package installed.
|
||||
Simulations should be run with 1 MPI task per physical {core},
|
||||
not {hardware thread}.
|
||||
|
||||
For Intel Xeon CPUs:
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
|
||||
If using {kspace_style pppm} in the input script, add "neigh_modify binsize cutoff" and "kspace_modify diff ad" to the input script for better
|
||||
performance. Cutoff should be roughly the neighbor list cutoff. By
|
||||
default the binsize is half the neighbor list cutoff. :l
|
||||
"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
|
||||
Set the environment variable KMP_BLOCKTIME=0 :l
|
||||
"-pk intel 0 omp $t -sf intel" added to LAMMPS command-line :l
|
||||
$t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
|
||||
For some of the simple 2-body potentials without long-range
|
||||
electrostatics, performance and scalability can be better with
|
||||
the "newton off" setting added to the input script :l
|
||||
If using {kspace_style pppm} in the input script, add
|
||||
"kspace_modify diff ad" for better performance :l
|
||||
:ule
|
||||
|
||||
For Intel Xeon Phi CPUs for simulations without {kspace_style
|
||||
pppm} in the input script :
|
||||
For Intel Xeon Phi CPUs:
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
|
||||
Runs should be performed using MCDRAM. :l
|
||||
"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
|
||||
should be added to the LAMMPS command-line. Choice for best
|
||||
performance will depend on the simulation. :l
|
||||
Runs should be performed using MCDRAM. :ulb,l
|
||||
:ule
|
||||
|
||||
For Intel Xeon Phi CPUs for simulations with {kspace_style
|
||||
pppm} in the input script:
|
||||
For simulations using {kspace_style pppm} on Intel CPUs
|
||||
supporting AVX-512:
|
||||
|
||||
Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
|
||||
Runs should be performed using MCDRAM. :l
|
||||
Add "neigh_modify binsize 3" to the input script for better
|
||||
performance. :l
|
||||
Add "kspace_modify diff ad" to the input script for better
|
||||
performance. :l
|
||||
export KMP_AFFINITY=none :l
|
||||
"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
|
||||
-sf intel" added to LAMMPS command-line. Choice for best performance
|
||||
will depend on the simulation. :l
|
||||
Add "kspace_modify diff ad" to the input script :ulb,l
|
||||
The command-line option should be changed to
|
||||
"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
|
||||
threads minus 1. :l
|
||||
Do not use thread affinity (set KMP_AFFINITY=none) :l
|
||||
The "newton off" setting may provide better scalability :l
|
||||
:ule
|
||||
|
||||
For Intel Xeon Phi coprocessors (Offload):
|
||||
@ -169,6 +195,10 @@ cat /proc/cpuinfo :pre
|
||||
|
||||
[Building LAMMPS with the USER-INTEL package:]
|
||||
|
||||
NOTE: See the src/USER-INTEL/README file for additional flags that
|
||||
might be needed for best performance on Intel server processors
|
||||
code-named "Skylake".
|
||||
|
||||
The USER-INTEL package must be installed into the source directory:
|
||||
|
||||
make yes-user-intel :pre
|
||||
@ -322,8 +352,8 @@ follow in the input script.
|
||||
|
||||
NOTE: The USER-INTEL package will perform better with modifications
|
||||
to the input script when "PPPM"_kspace_style.html is used:
|
||||
"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize
|
||||
3"_neigh_modify.html should be added to the input script.
|
||||
"kspace_modify diff ad"_kspace_modify.html should be added to the
|
||||
input script.
|
||||
|
||||
Long-Range Thread (LRT) mode is an option to the "package
|
||||
intel"_package.html command that can improve performance when using
|
||||
@ -342,6 +372,10 @@ would normally perform best with "-pk intel 0 omp 4", instead use
|
||||
environment variable "KMP_AFFINITY=none". LRT mode is not supported
|
||||
when using offload.
|
||||
|
||||
NOTE: Changing the "newton"_newton.html setting to off can improve
|
||||
performance and/or scalability for simple 2-body potentials such as
|
||||
lj/cut or when using LRT mode on processors supporting AVX-512.
|
||||
|
||||
Not all styles are supported in the USER-INTEL package. You can mix
|
||||
the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
|
||||
package or the "USER-OMP package"_accelerate_omp.html. Of course,
|
||||
@ -467,7 +501,7 @@ supported.
|
||||
|
||||
Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
|
||||
|
||||
Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
|
||||
Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l
|
||||
|
||||
Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l
|
||||
:ule
|
||||
|
||||
@ -30,7 +30,7 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
|
||||
|
||||
to define a modified finite extensible nonlinear elastic (FENE) potential
|
||||
"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
|
||||
in the oxDNA force field for coarse-grained modelling of DNA.
|
||||
in the oxDNA force field for coarse-grained modelling of DNA.
|
||||
|
||||
The following coefficients must be defined for the bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as given in the above example, or in
|
||||
@ -43,8 +43,8 @@ r0 (distance) :ul
|
||||
|
||||
NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles
|
||||
for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
|
||||
and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
|
||||
"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair
|
||||
and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
|
||||
"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair
|
||||
style {oxdna2/dh} have to be defined.
|
||||
The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
|
||||
|
||||
@ -66,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
|
||||
"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
||||
@ -42,7 +42,7 @@ where the index {j} goes over the {n}i nearest neighbors of atom
|
||||
{i}, and the index {k} goes over the {n}ij common nearest neighbors
|
||||
between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom
|
||||
{k} to atoms {i} and {j}. The quantity in the double sum is computed
|
||||
for each atom.
|
||||
for each atom.
|
||||
|
||||
The CNP calculation is sensitive to the specified cutoff value.
|
||||
You should ensure that the appropriate nearest neighbors of an atom are
|
||||
|
||||
@ -76,7 +76,9 @@ command for the types of the two atoms is used. For the {radius}
|
||||
setting, the sum of the radii of the two particles is used as a
|
||||
cutoff. For example, this is appropriate for granular particles which
|
||||
only interact when they are overlapping, as computed by "granular pair
|
||||
styles"_pair_gran.txt.
|
||||
styles"_pair_gran.txt. Note that if a granular model defines atom
|
||||
types such that all particles of a specific type are monodisperse
|
||||
(same diameter), then the two settings are effectively identical.
|
||||
|
||||
Note that as atoms migrate from processor to processor, there will be
|
||||
no consistent ordering of the entries within the local vector or array
|
||||
|
||||
@ -79,6 +79,9 @@ the two atoms is used. For the {radius} setting, the sum of the radii
|
||||
of the two particles is used as a cutoff. For example, this is
|
||||
appropriate for granular particles which only interact when they are
|
||||
overlapping, as computed by "granular pair styles"_pair_gran.html.
|
||||
Note that if a granular model defines atom types such that all
|
||||
particles of a specific type are monodisperse (same diameter), then
|
||||
the two settings are effectively identical.
|
||||
|
||||
If the inputs are bond, angle, etc attributes, the local data is
|
||||
generated by looping over all the atoms owned on a processor and
|
||||
|
||||
@ -138,7 +138,15 @@ more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This dihedral style can only be used if LAMMPS was built with the
|
||||
When using run_style "respa"_run_style.html, these dihedral styles
|
||||
must be assigned to the same r-RESPA level as {pair} or {outer}.
|
||||
|
||||
When used in combination with CHARMM pair styles, the 1-4
|
||||
"special_bonds"_special_bonds.html scaling factors must be set to 0.0.
|
||||
Otherwise non-bonded contributions for these 1-4 pairs will be
|
||||
computed multiple times.
|
||||
|
||||
These dihedral styles can only be used if LAMMPS was built with the
|
||||
MOLECULE package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
|
||||
@ -16,7 +16,7 @@ ID = user-assigned name for the dump
|
||||
group-ID = ID of the group of atoms to be dumped
|
||||
vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page)
|
||||
N = dump every this many timesteps
|
||||
file = name of file to write dump info to
|
||||
file = name of file to write dump info to
|
||||
args = same as arguments for "dump_style custom"_dump.html :ul
|
||||
|
||||
[Examples:]
|
||||
@ -83,7 +83,7 @@ Triclinic simulation boxes (non-orthogonal) are saved as
|
||||
hexahedrons in either legacy .vtk or .vtu XML format.
|
||||
|
||||
Style {vtk} allows you to specify a list of atom attributes to be
|
||||
written to the dump file for each atom. The list of possible attributes
|
||||
written to the dump file for each atom. The list of possible attributes
|
||||
is the same as for the "dump_style custom"_dump.html command; see
|
||||
its doc page for a listing and an explanation of each attribute.
|
||||
|
||||
|
||||
@ -245,7 +245,7 @@ appear the system is converging to your specified pressure. The
|
||||
solution for this is to either (a) zero the velocities of all atoms
|
||||
before performing the minimization, or (b) make sure you are
|
||||
monitoring the pressure without its kinetic component. The latter can
|
||||
be done by outputting the pressure from the pressure compute this
|
||||
be done by outputting the pressure from the pressure compute this
|
||||
command creates (see below) or a pressure compute you define yourself.
|
||||
|
||||
NOTE: Because pressure is often a very sensitive function of volume,
|
||||
|
||||
@ -45,14 +45,14 @@ species {j} in particle {i}, {u_j} is the internal energy of species j,
|
||||
{DeltaH_f,j} is the heat of formation of species {j}, N is the number of
|
||||
molecules represented by the coarse-grained particle, kb is the
|
||||
Boltzmann constant, and T is the temperature of the system. Additionally,
|
||||
it is possible to modify the concentration-dependent particle internal
|
||||
energy relation by adding an energy correction, temperature-dependent
|
||||
it is possible to modify the concentration-dependent particle internal
|
||||
energy relation by adding an energy correction, temperature-dependent
|
||||
correction, and/or a molecule-dependent correction. An energy correction can
|
||||
be specified as a constant (in energy units). A temperature correction can be
|
||||
specified by multiplying a temperature correction coefficient by the
|
||||
internal temperature. A molecular correction can be specified by
|
||||
by multiplying a molecule correction coefficient by the average number of
|
||||
product gas particles in the coarse-grain particle.
|
||||
be specified as a constant (in energy units). A temperature correction can be
|
||||
specified by multiplying a temperature correction coefficient by the
|
||||
internal temperature. A molecular correction can be specified by
|
||||
by multiplying a molecule correction coefficient by the average number of
|
||||
product gas particles in the coarse-grain particle.
|
||||
|
||||
Fix {eos/table/rx} creates interpolation tables of length {N} from {m}
|
||||
internal energy values of each species {u_j} listed in a file as a
|
||||
@ -72,12 +72,12 @@ The second filename specifies a file containing heat of formation
|
||||
{DeltaH_f,j} for each species.
|
||||
|
||||
In cases where the coarse-grain particle represents a single molecular
|
||||
species (i.e., no reactions occur and fix {rx} is not present in the input file),
|
||||
fix {eos/table/rx} can be applied in a similar manner to fix {eos/table}
|
||||
within a non-reactive DPD simulation. In this case, the heat of formation
|
||||
species (i.e., no reactions occur and fix {rx} is not present in the input file),
|
||||
fix {eos/table/rx} can be applied in a similar manner to fix {eos/table}
|
||||
within a non-reactive DPD simulation. In this case, the heat of formation
|
||||
filename is replaced with the heat of formation value for the single species.
|
||||
Additionally, the energy correction and temperature correction coefficients may
|
||||
also be specified as fix arguments.
|
||||
Additionally, the energy correction and temperature correction coefficients may
|
||||
also be specified as fix arguments.
|
||||
|
||||
:line
|
||||
|
||||
@ -138,8 +138,8 @@ used as the species name must correspond with the tags used to define
|
||||
the reactions with the "fix rx"_fix_rx.html command.
|
||||
|
||||
Alternatively, corrections to the EOS can be included by specifying
|
||||
three additional columns that correspond to the energy correction,
|
||||
the temperature correction coefficient and molecule correction
|
||||
three additional columns that correspond to the energy correction,
|
||||
the temperature correction coefficient and molecule correction
|
||||
coefficient. In this case, the format of the file is as follows:
|
||||
|
||||
# HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre
|
||||
|
||||
@ -70,8 +70,8 @@ minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Currently, it does not support "molecule templates"_molecule.html.
|
||||
|
||||
@ -406,7 +406,7 @@ the user for each subsequent fix gcmc command.
|
||||
[Default:]
|
||||
|
||||
The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
|
||||
fugacity_coeff = 1, and full_energy = no,
|
||||
fugacity_coeff = 1, and full_energy = no,
|
||||
except for the situations where full_energy is required, as
|
||||
listed above.
|
||||
|
||||
|
||||
@ -85,13 +85,13 @@ No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
The "thermo_modify"_thermo_modify.html {press} option is supported
|
||||
by this fix to add the rescaled kinetic pressure as part of
|
||||
by this fix to add the rescaled kinetic pressure as part of
|
||||
"thermodynamic output"_thermo_style.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
@ -58,14 +58,14 @@ input are listed in the same order as in the data file of LAMMPS. The
|
||||
initial configuration is ignored, as it will be substituted with the
|
||||
coordinates received from i-PI before forces are ever evaluated.
|
||||
|
||||
A note of caution when using potentials that contain long-range
|
||||
A note of caution when using potentials that contain long-range
|
||||
electrostatics, or that contain parameters that depend on box size:
|
||||
all of these options will be initialized based on the cell size in the
|
||||
LAMMPS-side initial configuration and kept constant during the run.
|
||||
This is required to e.g. obtain reproducible and conserved forces.
|
||||
If the cell varies too wildly, it may be advisable to reinitialize
|
||||
these interactions at each call. This behavior can be requested by
|
||||
setting the {reset} switch.
|
||||
LAMMPS-side initial configuration and kept constant during the run.
|
||||
This is required to e.g. obtain reproducible and conserved forces.
|
||||
If the cell varies too wildly, it may be advisable to reinitialize
|
||||
these interactions at each call. This behavior can be requested by
|
||||
setting the {reset} switch.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
|
||||
@ -57,7 +57,7 @@ simulations is as follows:
|
||||
Perform all-atom simulations on the system to be coarse grained.
|
||||
Generate a trajectory mapped to the coarse-grained model.
|
||||
Create input files for the MS-CG library.
|
||||
Run the range finder functionality of the MS-CG library.
|
||||
Run the range finder functionality of the MS-CG library.
|
||||
Run the force matching functionality of the MS-CG library.
|
||||
Check the results of the force matching.
|
||||
Run coarse-grained simulations using the new coarse-grained potentials. :ol
|
||||
@ -70,7 +70,7 @@ Step 2 can be performed using a Python script (what is the name?)
|
||||
provided with the MS-CG library which defines the coarse-grained model
|
||||
and converts a standard LAMMPS dump file for an all-atom simulation
|
||||
(step 1) into a LAMMPS dump file which has the positions of and forces
|
||||
on the coarse-grained beads.
|
||||
on the coarse-grained beads.
|
||||
|
||||
In step 3, an input file named "control.in" is needed by the MS-CG
|
||||
library which sets parameters for the range finding and force matching
|
||||
|
||||
@ -14,152 +14,179 @@ fix ID group-ID neb Kspring keyword value :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
neb = style name of this fix command :l
|
||||
Kspring = parallel spring constant (force/distance units or force units) :l
|
||||
Kspring = spring constant for parallel nudging force (force/distance units or force units, see parallel keyword) :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {nudg_style} or {perp} or {freend} or {freend_k_spring} :l
|
||||
{nudg_style} value = {neigh} or {idealpos}
|
||||
{neigh} = the parallel nudging force is calculated from the distances to neighbouring replicas (in this case, Kspring is in force/distance units)
|
||||
{idealpos} = the parallel nudging force is proportional to the distance between the replica and its interpolated ideal position (in this case Kspring is in force units)
|
||||
{perp} value {none} or kspring2
|
||||
{none} = no perpendicular spring force is applied
|
||||
{kspring2} = spring constant for the perpendicular nudging force (in force/distance units)
|
||||
{freeend} value = {none} or {ini} or {final} or {finaleini} or {final2eini}
|
||||
{none} = no nudging force is applied to the first and last replicas
|
||||
{ini} = set the first replica to be a free end
|
||||
{final} = set the last replica to be a free end
|
||||
{finaleini} = set the last replica to be a free end and set its target energy as that of the first replica
|
||||
{final2eini} = same as {finaleini} plus prevent intermediate replicas to have a lower energy than the first replica
|
||||
{freeend_kspring} value = kspring3
|
||||
kspring3 = spring constant of the perpendicular spring force (per distance units)
|
||||
:pre
|
||||
keyword = {parallel} or {perp} or {end} :l
|
||||
{parallel} value = {neigh} or {ideal}
|
||||
{neigh} = parallel nudging force based on distance to neighbor replicas (Kspring = force/distance units)
|
||||
{ideal} = parallel nudging force based on interpolated ideal position (Kspring = force units)
|
||||
{perp} value = {Kspring2}
|
||||
{Kspring2} = spring constant for perpendicular nudging force (force/distance units)
|
||||
{end} values = estyle Kspring3
|
||||
{estyle} = {first} or {last} or {last/efirst} or {last/efirst/middle}
|
||||
{first} = apply force to first replica
|
||||
{last} = apply force to last replica
|
||||
{last/efirst} = apply force to last replica and set its target energy to that of first replica
|
||||
{last/efirst/middle} = same as {last/efirst} plus prevent middle replicas having lower energy than first replica
|
||||
{Kspring3} = spring constant for target energy term (1/distance units) :pre,ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 active neb 10.0
|
||||
fix 2 all neb 1.0 perp 1.0 freeend final
|
||||
fix 1 all neb 1.0 nudg_style idealpos freeend final2eini freend_kspring 1:pre
|
||||
fix 2 all neb 1.0 perp 1.0 end last
|
||||
fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0
|
||||
fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Add a nudging force to atoms in the group for a multi-replica
|
||||
Add nudging forces to atoms in the group for a multi-replica
|
||||
simulation run via the "neb"_neb.html command to perform a nudged
|
||||
elastic band (NEB) calculation for finding the transition state.
|
||||
Hi-level explanations of NEB are given with the "neb"_neb.html command
|
||||
and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
|
||||
The fix neb command must be used with the "neb" command and defines
|
||||
how nudging inter-replica forces are computed. A NEB calculation is
|
||||
how inter-replica nudging forces are computed. A NEB calculation is
|
||||
divided in two stages. In the first stage n replicas are relaxed
|
||||
toward a MEP and in a second stage, the climbing image scheme (see
|
||||
"(Henkelman2)"_#Henkelman2) is turned on so that the replica having
|
||||
the highest energy relaxes toward the saddle point (i.e. the point of
|
||||
highest energy along the MEP).
|
||||
toward a MEP until convergence. In the second stage, the climbing
|
||||
image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the
|
||||
replica having the highest energy relaxes toward the saddle point
|
||||
(i.e. the point of highest energy along the MEP), and a second
|
||||
relaxation is performed.
|
||||
|
||||
One purpose of the nudging forces is to keep the replicas equally
|
||||
spaced. During the NEB, the 3N-length vector of interatomic force Fi
|
||||
= -Grad(V) of replicas i is altered. For all intermediate replicas
|
||||
(i.e. for 1<i<n) but the climbing replica the force vector
|
||||
becomes:
|
||||
A key purpose of the nudging forces is to keep the replicas equally
|
||||
spaced. During the NEB calculation, the 3N-length vector of
|
||||
interatomic force Fi = -Grad(V) for each replica I is altered. For
|
||||
all intermediate replicas (i.e. for 1 < I < N, except the climbing
|
||||
replica) the force vector becomes:
|
||||
|
||||
Fi = -Grad(V) + (Grad(V) dot That) That + Fnudgparallel + Fspringperp :pre
|
||||
Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp :pre
|
||||
|
||||
That is the unit "tangent" vector for replica i and is a function of
|
||||
Ri, Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
|
||||
roughly in the direction of (Ri+i - Ri-1) (see the
|
||||
"(Henkelman1)"_#Henkelman1 paper for details). Ri are the atomic
|
||||
coordinates of replica i; Ri-1 and Ri+1 are the coordinates of its
|
||||
neighbor replicas. The term (Grad(V) dot That) is used to remove the
|
||||
T' is the unit "tangent" vector for replica I and is a function of Ri,
|
||||
Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
|
||||
roughly in the direction of (Ri+i - Ri-1); see the
|
||||
"(Henkelman1)"_#Henkelman1 paper for details. Ri are the atomic
|
||||
coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its
|
||||
neighbor replicas. The term (Grad(V) dot T') is used to remove the
|
||||
component of the gradient parallel to the path which would tend to
|
||||
distribute the replica unevenly along the path. Fnudgparallel is an
|
||||
artificial nudging force which is applied only in the tangent direction
|
||||
and which maintains the replicas equally spaced (see below for more
|
||||
information). Fspringperp is an optinal artificial spring which is
|
||||
applied only perpendicular to the tangent and which prevent the paths
|
||||
from forming too acute kinks (see below for more information).
|
||||
distribute the replica unevenly along the path. Fnudge_parallel is an
|
||||
artificial nudging force which is applied only in the tangent
|
||||
direction and which maintains the equal spacing between replicas (see
|
||||
below for more information). Fnudge_perp is an optional artificial
|
||||
spring which is applied in a direction perpendicular to the tangent
|
||||
direction and which prevent the paths from forming acute kinks (see
|
||||
below for more information).
|
||||
|
||||
The keyword {nudg_style} allow to specify how to parallel
|
||||
nudging force is computed. With a value of idealpos, the spring
|
||||
force is computed as suggested in "(E)"_#E :
|
||||
|
||||
Fnudgparallel=-{Kspring}* (RD-RDideal)/(2 meanDist) :pre
|
||||
In the second stage of the NEB calculation, the interatomic force Fi
|
||||
for the climbing replica (the replica of highest energy after the
|
||||
first stage) is changed to:
|
||||
|
||||
Fi = -Grad(V) + 2 (Grad(V) dot T') T' :pre
|
||||
|
||||
and the relaxation procedure is continued to a new converged MEP.
|
||||
|
||||
:line
|
||||
|
||||
The keyword {parallel} specifies how the parallel nudging force is
|
||||
computed. With a value of {neigh}, the parallel nudging force is
|
||||
computed as in "(Henkelman1)"_#Henkelman1 by connecting each
|
||||
intermediate replica with the previous and the next image:
|
||||
|
||||
Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
|
||||
|
||||
Note that in this case the specified {Kspring) is in force/distance
|
||||
units.
|
||||
|
||||
With a value of {ideal}, the spring force is computed as suggested in
|
||||
"(WeinenE)"_#WeinenE :
|
||||
|
||||
Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
|
||||
|
||||
where RD is the "reaction coordinate" see "neb"_neb.html section, and
|
||||
RDideal is the ideal RD for which all the images are equally spaced
|
||||
(i.e. RDideal = (i-1)*meanDist when the climbing image is off, where i
|
||||
is the replica number). The meanDist is the average distance between
|
||||
replicas.
|
||||
RDideal is the ideal RD for which all the images are equally spaced.
|
||||
I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
|
||||
I is the replica number). The meanDist is the average distance
|
||||
between replicas. Note that in this case the specified {Kspring) is
|
||||
in force units.
|
||||
|
||||
When {nudg_style} has a value of neigh (or by default), the parallel
|
||||
nudging force is computed as in "(Henkelman1)"_#Henkelman1 by
|
||||
connecting each intermediate replica with the previous and the next
|
||||
image:
|
||||
|
||||
Fnudgparallel= {Kspring}* (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
|
||||
|
||||
The parallel nudging force associated with the key word idealpos should
|
||||
usually be more efficient at keeping the images equally spaced.
|
||||
Note that the {ideal} form of nudging can often be more effective at
|
||||
keeping the replicas equally spaced.
|
||||
|
||||
:line
|
||||
|
||||
The keyword {perp} allows to add a spring force perpendicular to the
|
||||
path in order to prevent the path from becoming too kinky. It can
|
||||
improve significantly the convergence of the NEB when the resolution
|
||||
is poor (i.e. when too few images are used) (see "(Maras)"_#Maras1).
|
||||
The keyword {perp} specifies if and how a perpendicual nudging force
|
||||
is computed. It adds a spring force perpendicular to the path in
|
||||
order to prevent the path from becoming too kinky. It can
|
||||
significantly improve the convergence of the NEB calculation when the
|
||||
resolution is poor. I.e. when few replicas are used; see
|
||||
"(Maras)"_#Maras1 for details.
|
||||
|
||||
The perpendicular spring force is given by
|
||||
|
||||
Fspringperp = {Kspringperp} * f(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
|
||||
Fnudge_perp = {Kspring2} * F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
|
||||
|
||||
f(Ri-1 Ri R+1) is a smooth scalar function of the angle Ri-1 Ri
|
||||
Ri+1. It is equal to 0 when the path is straight and is equal to 1
|
||||
when the angle Ri-1 Ri Ri+1 is accute. f(Ri-1 Ri R+1) is defined in
|
||||
"(Jonsson)"_#Jonsson
|
||||
where {Kspring2} is the specified value. F(Ri-1 Ri R+1) is a smooth
|
||||
scalar function of the angle Ri-1 Ri Ri+1. It is equal to 0.0 when
|
||||
the path is straight and is equal to 1 when the angle Ri-1 Ri Ri+1 is
|
||||
acute. F(Ri-1 Ri R+1) is defined in "(Jonsson)"_#Jonsson.
|
||||
|
||||
If {Kspring2} is set to 0.0 (the default) then no perpendicular spring
|
||||
force is added.
|
||||
|
||||
:line
|
||||
|
||||
By default, the force acting on the first and last replicas is not
|
||||
altered so that during the NEB relaxation, these ending replicas relax
|
||||
toward local minima. However it is possible to use the key word
|
||||
{freeend} to allow either the initial or the final replica to relax
|
||||
toward a MEP while constraining its energy. The interatomic force Fi
|
||||
for the free end image becomes :
|
||||
By default, no additional forces act on the first and last replicas
|
||||
during the NEB relaxation, so these replicas simply relax toward their
|
||||
respective local minima. By using the key word {end}, additional
|
||||
forces can be applied to the first and/or last replicas, to enable
|
||||
them to relax toward a MEP while constraining their energy.
|
||||
|
||||
Fi = -Grad(V)+ (Grad(V) dot That + (E-ETarget)*kspring3) That, {when} Grad(V) dot That < 0
|
||||
Fi = -Grad(V)+ (Grad(V) dot That + (ETarget- E)*kspring3) That, {when} Grad(V) dot That > 0
|
||||
The interatomic force Fi for the specified replica becomes:
|
||||
|
||||
Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T', {when} Grad(V) dot T' < 0
|
||||
Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0
|
||||
:pre
|
||||
|
||||
where E is the energy of the free end replica and ETarget is the
|
||||
target energy.
|
||||
where E is the current energy of the replica and ETarget is the target
|
||||
energy. The "spring" constant on the difference in energies is the
|
||||
specified {Kspring3} value.
|
||||
|
||||
When the value {ini} ({final}) is used after the keyword {freeend},
|
||||
the first (last) replica is considered as a free end. The target
|
||||
energy is set to the energy of the replica at starting of the NEB
|
||||
calculation. When the value {finaleini} or {final2eini} is used the
|
||||
last image is considered as a free end and the target energy is equal
|
||||
to the energy of the first replica (which can evolve during the NEB
|
||||
relaxation). With the value {finaleini}, when the initial path is too
|
||||
far from the MEP, an intermediate repilica might relax "faster" and
|
||||
get a lower energy than the last replica. The benefit of the free end
|
||||
is then lost since this intermediate replica will relax toward a local
|
||||
minima. This behavior can be prevented by using the value {final2eini}
|
||||
which remove entirely the contribution of the gradient for all
|
||||
intermediate replica which have a lower energy than the initial one
|
||||
thus preventing these replicae to over-relax. After converging a NEB
|
||||
with the {final2eini} value it is recommended to check that all
|
||||
intermediate replica have a larger energy than the initial
|
||||
replica. Finally note that if the last replica converges toward a
|
||||
local minimum with a larger energy than the energy of the first
|
||||
replica, a free end neb calculation with the value {finaleini} or
|
||||
{final2eini} cannot reach the convergence criteria.
|
||||
When {estyle} is specified as {first}, the force is applied to the
|
||||
first replica. When {estyle} is specified as {last}, the force is
|
||||
applied to the last replica. Note that the {end} keyword can be used
|
||||
twice to add forces to both the first and last replicas.
|
||||
|
||||
:line
|
||||
For both these {estyle} settings, the target energy {ETarget} is set
|
||||
to the initial energy of the replica (at the start of the NEB
|
||||
calculation).
|
||||
|
||||
If the {estyle} is specified as {last/efirst} or {last/efirst/middle},
|
||||
force is applied to the last replica, but the target energy {ETarget}
|
||||
is continuously set to the energy of the first replica, as it evolves
|
||||
during the NEB relaxation.
|
||||
|
||||
The difference between these two {estyle} options is as follows. When
|
||||
{estyle} is specified as {last/efirst}, no change is made to the
|
||||
inter-replica force applied to the intermediate replicas (neither
|
||||
first or last). If the initial path is too far from the MEP, an
|
||||
intermediate repilica may relax "faster" and reach a lower energy than
|
||||
the last replica. In this case the intermediate replica will be
|
||||
relaxing toward its own local minima. This behavior can be prevented
|
||||
by specifying {estyle} as {last/efirst/middle} which will alter the
|
||||
inter-replica force applied to intermediate replicas by removing the
|
||||
contribution of the gradient to the inter-replica force. This will
|
||||
only be done if a particular intermediate replica has a lower energy
|
||||
than the first replica. This should effectively prevent the
|
||||
intermediate replicas from over-relaxing.
|
||||
|
||||
In the second stage of the NEB, the interatomic force Fi for the
|
||||
climbing replica (which is the replica of highest energy) becomes:
|
||||
|
||||
Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
|
||||
|
||||
After converging a NEB calculation using an {estyle} of
|
||||
{last/efirst/middle}, you should check that all intermediate replicas
|
||||
have a larger energy than the first replica. If this is not the case,
|
||||
the path is probably not a MEP.
|
||||
|
||||
Finally, note that if the last replica converges toward a local
|
||||
minimum which has a larger energy than the energy of the first
|
||||
replica, a NEB calculation using an {estyle} of {last/efirst} or
|
||||
{last/efirst/middle} cannot reach final convergence.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
@ -186,7 +213,8 @@ for more info on packages.
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are nudg_style = neigh, perp = none, freeend = none and freend_kspring = 1.
|
||||
The option defaults are nudge = neigh, perp = 0.0, ends is not
|
||||
specified (no inter-replica force on the end replicas).
|
||||
|
||||
:line
|
||||
|
||||
@ -197,14 +225,14 @@ The option defaults are nudg_style = neigh, perp = none, freeend = none and free
|
||||
[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
|
||||
9901-9904 (2000).
|
||||
|
||||
:link(E)
|
||||
[(E)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002)
|
||||
:link(WeinenE)
|
||||
[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
|
||||
|
||||
:link(Jonsson)
|
||||
[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum
|
||||
Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, and Coker
|
||||
World Scientific, Singapore, 1998, p. 385
|
||||
Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti,
|
||||
and Coker World Scientific, Singapore, 1998, p 385.
|
||||
|
||||
:link(Maras1)
|
||||
[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
|
||||
Comp Phys Comm, 205, 13-21 (2016)
|
||||
Comp Phys Comm, 205, 13-21 (2016).
|
||||
|
||||
@ -23,13 +23,13 @@ fix 1 all nve/dot :pre
|
||||
[Description:]
|
||||
|
||||
Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
|
||||
to a group of atoms, but without Langevin dynamics.
|
||||
to a group of atoms, but without Langevin dynamics.
|
||||
This command performs Molecular dynamics (MD)
|
||||
via a velocity-Verlet algorithm and an evolution operator that rotates
|
||||
the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
|
||||
via a velocity-Verlet algorithm and an evolution operator that rotates
|
||||
the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
|
||||
|
||||
This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
without damping and noise and can be used to determine the stability range
|
||||
without damping and noise and can be used to determine the stability range
|
||||
in a NVE ensemble prior to using the Langevin-type DOTC-integrator
|
||||
(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
|
||||
The command is equivalent to the "fix nve"_fix_nve.html.
|
||||
|
||||
@ -28,20 +28,20 @@ fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
|
||||
Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
|
||||
as described in "(Davidchack)"_#Davidchack2
|
||||
to a group of atoms, which models an interaction with an implicit background
|
||||
solvent. This command performs Brownian dynamics (BD)
|
||||
via a technique that splits the integration into a deterministic Hamiltonian
|
||||
part and the Ornstein-Uhlenbeck process for noise and damping.
|
||||
via a technique that splits the integration into a deterministic Hamiltonian
|
||||
part and the Ornstein-Uhlenbeck process for noise and damping.
|
||||
The quaternion degrees of freedom are updated though an evolution
|
||||
operator which performs a rotation in quaternion space, preserves
|
||||
the quaternion norm and is akin to "(Miller)"_#Miller2.
|
||||
|
||||
In terms of syntax this command has been closely modelled on the
|
||||
"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
|
||||
the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
|
||||
one single command. The main feature is improved stability
|
||||
In terms of syntax this command has been closely modelled on the
|
||||
"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
|
||||
the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
|
||||
one single command. The main feature is improved stability
|
||||
over the standard integrator, permitting slightly larger timestep sizes.
|
||||
|
||||
NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
|
||||
@ -57,7 +57,7 @@ Fc is the conservative force computed via the usual inter-particle
|
||||
interactions ("pair_style"_pair_style.html,
|
||||
"bond_style"_bond_style.html, etc).
|
||||
|
||||
The Ff and Fr terms are implicitly taken into account by this fix
|
||||
The Ff and Fr terms are implicitly taken into account by this fix
|
||||
on a per-particle basis.
|
||||
|
||||
Ff is a frictional drag or viscous damping term proportional to the
|
||||
@ -77,7 +77,7 @@ a Gaussian random number) for speed.
|
||||
|
||||
:line
|
||||
|
||||
{Tstart} and {Tstop} have to be constant values, i.e. they cannot
|
||||
{Tstart} and {Tstop} have to be constant values, i.e. they cannot
|
||||
be variables.
|
||||
|
||||
The {damp} parameter is specified in time units and determines how
|
||||
@ -98,16 +98,16 @@ different numbers of processors.
|
||||
|
||||
The keyword/value option has to be used in the following way:
|
||||
|
||||
This fix has to be used together with the {angmom} keyword. The
|
||||
particles are always considered to have a finite size.
|
||||
The keyword {angmom} enables thermostatting of the rotational degrees of
|
||||
freedom in addition to the usual translational degrees of freedom.
|
||||
This fix has to be used together with the {angmom} keyword. The
|
||||
particles are always considered to have a finite size.
|
||||
The keyword {angmom} enables thermostatting of the rotational degrees of
|
||||
freedom in addition to the usual translational degrees of freedom.
|
||||
|
||||
The scale factor after the {angmom} keyword gives the ratio of the rotational to
|
||||
The scale factor after the {angmom} keyword gives the ratio of the rotational to
|
||||
the translational friction coefficient.
|
||||
|
||||
An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
|
||||
A technical report with more information on this integrator can be found
|
||||
A technical report with more information on this integrator can be found
|
||||
"here"_PDF/USER-CGDNA-overview.pdf.
|
||||
|
||||
:line
|
||||
@ -120,7 +120,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
|
||||
"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
||||
@ -27,7 +27,7 @@ timestep. V is volume; K is kinetic energy. This creates a system
|
||||
trajectory consistent with the isokinetic ensemble.
|
||||
|
||||
The equations of motion used are those of Minary et al in
|
||||
"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in
|
||||
"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in
|
||||
"(Zhang)"_#nvk-Zhang.
|
||||
|
||||
The kinetic energy will be held constant at its value given when fix
|
||||
|
||||
@ -89,7 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
|
||||
group can straddle a periodic boundary. See the "dump"_dump.html doc
|
||||
page for a discussion of unwrapped coordinates. It also means that a
|
||||
spring connecting two groups or a group and the tether point can cross
|
||||
a periodic boundary and its length be calculated correctly.
|
||||
a periodic boundary and its length be calculated correctly.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
|
||||
@ -144,7 +144,11 @@ this fix.
|
||||
|
||||
"fix spring"_fix_spring.html, "fix adapt"_fix_adapt.html
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Default:]
|
||||
|
||||
|
||||
@ -219,10 +219,10 @@ instead of using the virial equation. This option cannot be used to access
|
||||
individual components of the pressure tensor, to compute per-atom virial,
|
||||
or with suffix kspace/pair styles of MSM, like OMP or GPU.
|
||||
|
||||
The {fftbench} keyword applies only to PPPM. It is on by default. If
|
||||
this option is turned off, LAMMPS will not take the time at the end
|
||||
of a run to give FFT benchmark timings, and will finish a few seconds
|
||||
faster than it would if this option were on.
|
||||
The {fftbench} keyword applies only to PPPM. It is off by default. If
|
||||
this option is turned on, LAMMPS will perform a short FFT benchmark
|
||||
computation and report its timings, and will thus finish a some seconds
|
||||
later than it would if this option were off.
|
||||
|
||||
The {collective} keyword applies only to PPPM. It is set to {no} by
|
||||
default, except on IBM BlueGene machines. If this option is set to
|
||||
@ -306,9 +306,10 @@ parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
|
||||
The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
|
||||
5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
|
||||
gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
|
||||
yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
|
||||
yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik
|
||||
(PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
|
||||
split = 0, tol = 1.0e-6, and disp/auto = no.
|
||||
split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order =
|
||||
order/disp = 7.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -33,12 +33,16 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/gpu} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/intel} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/kk} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/cg/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/disp/intel} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/tip4p/omp} value = accuracy
|
||||
accuracy = desired relative error in forces
|
||||
{pppm/stagger} value = accuracy
|
||||
|
||||
@ -344,7 +344,7 @@ informations can help understanding what is going wrong. For instance
|
||||
when the path angle becomes accute the definition of tangent used in
|
||||
the NEB calculation is questionable and the NEB cannot may diverge
|
||||
"(Maras)"_#Maras2.
|
||||
|
||||
|
||||
|
||||
When running on multiple partitions, LAMMPS produces additional log
|
||||
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
|
||||
|
||||
@ -40,8 +40,8 @@ vectorial atomic forces.
|
||||
|
||||
Only a single pair_coeff command is used with the {agni} style which
|
||||
specifies an AGNI potential file containing the parameters of the
|
||||
force field for the needed elements. These are mapped to LAMMPS atom
|
||||
types by specifying N additional arguments after the filename in the
|
||||
force field for the needed elements. These are mapped to LAMMPS atom
|
||||
types by specifying N additional arguments after the filename in the
|
||||
pair_coeff command, where N is the number of LAMMPS atom types:
|
||||
|
||||
filename
|
||||
@ -52,13 +52,13 @@ to specify the path for the force field file.
|
||||
|
||||
An AGNI force field is fully specified by the filename which contains the
|
||||
parameters of the force field, i.e., the reference training environments
|
||||
used to construct the machine learning force field. Example force field
|
||||
and input files are provided in the examples/USER/misc/agni directory.
|
||||
used to construct the machine learning force field. Example force field
|
||||
and input files are provided in the examples/USER/misc/agni directory.
|
||||
|
||||
:line
|
||||
|
||||
Styles with {omp} suffix is functionally the same as the corresponding
|
||||
style without the suffix. They have been optimized to run faster, depending
|
||||
Styles with {omp} suffix is functionally the same as the corresponding
|
||||
style without the suffix. They have been optimized to run faster, depending
|
||||
on your available hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated style takes the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
|
||||
@ -75,7 +75,7 @@ Lennard-Jones 12/6) given by
|
||||
:c,image(Eqs/pair_buck.jpg)
|
||||
|
||||
where rho is an ionic-pair dependent length parameter, and Rc is the
|
||||
cutoff on both terms.
|
||||
cutoff on both terms.
|
||||
|
||||
The styles with {coul/cut} or {coul/long} or {coul/msm} add a
|
||||
Coulombic term as described for the "lj/cut"_pair_lj.html pair styles.
|
||||
|
||||
@ -104,7 +104,15 @@ charmmfsw"_dihedral_charmm.html command. Eventually code from the new
|
||||
styles will propagate into the related pair styles (e.g. implicit,
|
||||
accelerator, free energy variants).
|
||||
|
||||
The general CHARMM formulas are as follows
|
||||
NOTE: The newest CHARMM pair styles reset the Coulombic energy
|
||||
conversion factor used internally in the code, from the LAMMPS value
|
||||
to the CHARMM value, as if it were effectively a parameter of the
|
||||
force field. This is because the CHARMM code uses a slightly
|
||||
different value for the this conversion factor in "real
|
||||
units"_units.html (Kcal/mole), namely CHARMM = 332.0716, LAMMPS =
|
||||
332.06371. This is to enable more precise agreement by LAMMPS with
|
||||
the CHARMM force field energies and forces, when using one of these
|
||||
two CHARMM pair styles.
|
||||
|
||||
:c,image(Eqs/pair_charmm.jpg)
|
||||
|
||||
|
||||
@ -71,6 +71,14 @@ and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
|
||||
torques do not act symmetrically. These formulas are discussed in
|
||||
"(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2.
|
||||
|
||||
Also note, that in the code, all of these terms (except Elj) have a
|
||||
C/epsilon prefactor, the same as the Coulombic term in the LJ +
|
||||
Coulombic pair styles discussed "here"_pair_lj.html. C is an
|
||||
energy-conversion constant and epsilon is the dielectric constant
|
||||
which can be set by the "dielectric"_dielectric.html command. The
|
||||
same is true of the equations that follow for other dipole pair
|
||||
styles.
|
||||
|
||||
Style {lj/sf/dipole/sf} computes "shifted-force" interactions between
|
||||
pairs of particles that each have a charge and/or a point dipole
|
||||
moment. In general, a shifted-force potential is a (sligthly) modified
|
||||
|
||||
@ -55,33 +55,33 @@ defined in the reaction kinetics files specified with the "fix
|
||||
rx"_fix_rx.html command or they must correspond to the tag "1fluid",
|
||||
signifying interaction with a product species mixture determined
|
||||
through a one-fluid approximation. The interaction potential is
|
||||
weighted by the geometric average of either the mole fraction concentrations
|
||||
or the number of molecules associated with the interacting coarse-grained
|
||||
particles (see the {fractional} or {molecular} weighting pair style options).
|
||||
weighted by the geometric average of either the mole fraction concentrations
|
||||
or the number of molecules associated with the interacting coarse-grained
|
||||
particles (see the {fractional} or {molecular} weighting pair style options).
|
||||
The coarse-grained potential is stored before and after the
|
||||
reaction kinetics solver is applied, where the difference is defined
|
||||
to be the internal chemical energy (uChem).
|
||||
|
||||
The fourth argument specifies the type of scaling that will be used
|
||||
The fourth argument specifies the type of scaling that will be used
|
||||
to scale the EXP-6 parameters as reactions occur. Currently, there
|
||||
are three scaling options: {exponent}, {polynomial} and {none}.
|
||||
|
||||
Exponent scaling requires two additional arguments for scaling
|
||||
Exponent scaling requires two additional arguments for scaling
|
||||
the {Rm} and {epsilon} parameters, respectively. The scaling factor
|
||||
is computed by phi^exponent, where phi is the number of molecules
|
||||
represented by the coarse-grain particle and exponent is specified
|
||||
is computed by phi^exponent, where phi is the number of molecules
|
||||
represented by the coarse-grain particle and exponent is specified
|
||||
as a pair coefficient argument for {Rm} and {epsilon}, respectively.
|
||||
The {Rm} and {epsilon} parameters are multiplied by the scaling
|
||||
The {Rm} and {epsilon} parameters are multiplied by the scaling
|
||||
factor to give the scaled interaction parameters for the CG particle.
|
||||
|
||||
Polynomial scaling requires a filename to be specified as a pair
|
||||
Polynomial scaling requires a filename to be specified as a pair
|
||||
coeff argument. The file contains the coefficients to a fifth order
|
||||
polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend
|
||||
upon phi (the number of molecules represented by the CG particle).
|
||||
polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend
|
||||
upon phi (the number of molecules represented by the CG particle).
|
||||
The format of a polynomial file is provided below.
|
||||
|
||||
The {none} option to the scaling does not have any additional pair coeff
|
||||
arguments. This is equivalent to specifying the {exponent} option with
|
||||
arguments. This is equivalent to specifying the {exponent} option with
|
||||
{Rm} and {epsilon} exponents of 0.0 and 0.0, respectively.
|
||||
|
||||
The final argument specifies the interaction cutoff (optional).
|
||||
@ -102,7 +102,7 @@ parenthesized comments):
|
||||
|
||||
# POLYNOMIAL FILE (one or more comment or blank lines) :pre
|
||||
# General Functional Form:
|
||||
# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F
|
||||
# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F
|
||||
#
|
||||
# Parameter A B C D E F
|
||||
(blank)
|
||||
|
||||
@ -24,25 +24,25 @@ pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
|
||||
potential as described in "(KC05)"_#KC05. An important simplification is made,
|
||||
which is to take all normals along the z-axis.
|
||||
The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
|
||||
potential as described in "(KC05)"_#KC05. An important simplification is made,
|
||||
which is to take all normals along the z-axis.
|
||||
|
||||
:c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
|
||||
|
||||
It is important to have a suffiently large cutoff to ensure smooth forces.
|
||||
Energies are shifted so that they go continously to zero at the cutoff assuming
|
||||
It is important to have a suffiently large cutoff to ensure smooth forces.
|
||||
Energies are shifted so that they go continously to zero at the cutoff assuming
|
||||
that the exponential part of {Vij} (first term) decays sufficiently fast.
|
||||
This shift is achieved by the last term in the equation for {Vij} above.
|
||||
|
||||
This potential is intended for interactions between two layers of graphene.
|
||||
Therefore, to avoid interaction between layers in multi-layered materials,
|
||||
each layer should have a separate atom type and interactions should only
|
||||
This potential is intended for interactions between two layers of graphene.
|
||||
Therefore, to avoid interaction between layers in multi-layered materials,
|
||||
each layer should have a separate atom type and interactions should only
|
||||
be computed between atom types of neighbouring layers.
|
||||
|
||||
The parameter file (e.g. CC.KC), is intended for use with metal
|
||||
"units"_units.html, with energies in meV. An additional parameter, {S},
|
||||
is available to facilitate scaling of energies in accordance with
|
||||
The parameter file (e.g. CC.KC), is intended for use with metal
|
||||
"units"_units.html, with energies in meV. An additional parameter, {S},
|
||||
is available to facilitate scaling of energies in accordance with
|
||||
"(vanWijk)"_#vanWijk.
|
||||
|
||||
This potential must be used in combination with hybrid/overlay.
|
||||
@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
:line
|
||||
|
||||
:link(KC05)
|
||||
:link(KC05)
|
||||
[(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
|
||||
|
||||
:link(vanWijk)
|
||||
|
||||
@ -7,6 +7,7 @@
|
||||
:line
|
||||
|
||||
pair_style lj/long/coul/long command :h3
|
||||
pair_style lj/long/coul/long/intel command :h3
|
||||
pair_style lj/long/coul/long/omp command :h3
|
||||
pair_style lj/long/coul/long/opt command :h3
|
||||
pair_style lj/long/tip4p/long command :h3
|
||||
|
||||
@ -104,3 +104,8 @@ This pair style can only be used via the {pair} keyword of the
|
||||
"pair_coeff"_pair_coeff.html, "pair lj/smooth"_pair_lj_smooth.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Toxvaerd)
|
||||
[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
|
||||
|
||||
@ -97,9 +97,9 @@ tags must either correspond to the species defined in the reaction
|
||||
kinetics files specified with the "fix rx"_fix_rx.html command or they
|
||||
must correspond to the tag "1fluid", signifying interaction with a
|
||||
product species mixture determined through a one-fluid approximation.
|
||||
The interaction potential is weighted by the geometric average of
|
||||
either the mole fraction concentrations or the number of molecules
|
||||
associated with the interacting coarse-grained particles (see the
|
||||
The interaction potential is weighted by the geometric average of
|
||||
either the mole fraction concentrations or the number of molecules
|
||||
associated with the interacting coarse-grained particles (see the
|
||||
{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
|
||||
stored before and after the reaction kinetics solver is applied, where
|
||||
the difference is defined to be the internal chemical energy (uChem).
|
||||
|
||||
@ -39,17 +39,17 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
|
||||
|
||||
[Description:]
|
||||
|
||||
The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
|
||||
and coaxial stacking interaction {oxdna/coaxstk} as well
|
||||
as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
|
||||
opposite strands.
|
||||
|
||||
The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
|
||||
in the above example. The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
|
||||
in the above example. The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
|
||||
for a detailed description of the oxDNA force field.
|
||||
|
||||
@ -57,8 +57,8 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty
|
||||
{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
|
||||
"bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
|
||||
The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
|
||||
When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
|
||||
The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
|
||||
When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
|
||||
or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
||||
@ -79,7 +79,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
|
||||
"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -45,17 +45,17 @@ pair_coeff * * oxdna2/dh 0.1 1.0 0.815 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
|
||||
and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
|
||||
as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
|
||||
opposite strands.
|
||||
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
|
||||
and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
|
||||
|
||||
@ -63,7 +63,7 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
|
||||
{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
|
||||
Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
|
||||
Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
|
||||
after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
|
||||
e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
@ -86,7 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
||||
[Related commands:]
|
||||
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
|
||||
"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
|
||||
"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
||||
@ -85,9 +85,9 @@ tags must either correspond to the species defined in the reaction
|
||||
kinetics files specified with the "fix rx"_fix_rx.html command or they
|
||||
must correspond to the tag "1fluid", signifying interaction with a
|
||||
product species mixture determined through a one-fluid approximation.
|
||||
The interaction potential is weighted by the geometric average of
|
||||
either the mole fraction concentrations or the number of molecules
|
||||
associated with the interacting coarse-grained particles (see the
|
||||
The interaction potential is weighted by the geometric average of
|
||||
either the mole fraction concentrations or the number of molecules
|
||||
associated with the interacting coarse-grained particles (see the
|
||||
{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
|
||||
stored before and after the reaction kinetics solver is applied, where
|
||||
the difference is defined to be the internal chemical energy (uChem).
|
||||
|
||||
@ -489,7 +489,7 @@ python"_Section_python.html. Note that it is important that the
|
||||
stand-alone LAMMPS executable and the LAMMPS shared library be
|
||||
consistent (built from the same source code files) in order for this
|
||||
to work. If the two have been built at different times using
|
||||
different source files, problems may occur.
|
||||
different source files, problems may occur.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
||||
@ -17,7 +17,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
|
||||
{verlet/split} args = none
|
||||
{respa} args = N n1 n2 ... keyword values ...
|
||||
N = # of levels of rRESPA
|
||||
n1, n2, ... = loop factor between rRESPA levels (N-1 values)
|
||||
n1, n2, ... = loop factors between rRESPA levels (N-1 values)
|
||||
zero or more keyword/value pairings may be appended to the loop factors
|
||||
keyword = {bond} or {angle} or {dihedral} or {improper} or
|
||||
{pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
|
||||
@ -55,7 +55,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
|
||||
|
||||
run_style verlet
|
||||
run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
|
||||
run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 :pre
|
||||
run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
|
||||
run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -86,7 +86,7 @@ machine via HTTPS:
|
||||
or, if you have set up your GitHub account for using SSH keys, via SSH:
|
||||
|
||||
$ git clone git@github.com:<your user name>/lammps.git :pre
|
||||
|
||||
|
||||
You can find the proper URL by clicking the "Clone or download"-button:
|
||||
|
||||
:c,image(JPG/tutorial_https_block.png)
|
||||
|
||||
@ -36,7 +36,7 @@ lammps.PyLammps :h4
|
||||
|
||||
higher-level abstraction built on top of original C-Types interface
|
||||
manipulation of Python objects
|
||||
communication with LAMMPS is hidden from API user
|
||||
communication with LAMMPS is hidden from API user
|
||||
shorter, more concise Python
|
||||
better IPython integration, designed for quick prototyping :ul
|
||||
|
||||
@ -328,7 +328,7 @@ IPyLammps Examples :h2
|
||||
|
||||
Examples of IPython notebooks can be found in the python/examples/pylammps
|
||||
subdirectory. To open these notebooks launch {jupyter notebook} inside this
|
||||
directory and navigate to one of them. If you compiled and installed
|
||||
directory and navigate to one of them. If you compiled and installed
|
||||
a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
|
||||
you should be able to rerun all of these notebooks.
|
||||
|
||||
@ -399,19 +399,19 @@ natoms = L.system.natoms :pre
|
||||
for i in range(niterations):
|
||||
iatom = random.randrange(0, natoms)
|
||||
current_atom = L.atoms\[iatom\] :pre
|
||||
|
||||
|
||||
x0, y0 = current_atom.position :pre
|
||||
|
||||
|
||||
dx = deltamove * random.uniform(-1, 1)
|
||||
dy = deltamove * random.uniform(-1, 1) :pre
|
||||
|
||||
|
||||
current_atom.position = (x0+dx, y0+dy) :pre
|
||||
|
||||
|
||||
L.run(1, "pre no post no") :pre
|
||||
|
||||
|
||||
e = L.eval("pe")
|
||||
energies.append(e) :pre
|
||||
|
||||
|
||||
if e <= elast:
|
||||
naccept += 1
|
||||
elast = e
|
||||
@ -460,4 +460,4 @@ Feedback and Contributing :h2
|
||||
If you find this Python interface useful, please feel free to provide feedback
|
||||
and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
|
||||
want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
|
||||
and maybe their latest research results.
|
||||
and maybe their latest research results.
|
||||
|
||||
@ -28,7 +28,7 @@ thermo 100
|
||||
thermo_style multi
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 pair 2 kspace 3
|
||||
run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
|
||||
|
||||
velocity all create 200.0 12345678 dist uniform
|
||||
#dump dump1 all atom 100 4pti.dump
|
||||
|
||||
@ -20,7 +20,7 @@ thermo 50
|
||||
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 pair 2 kspace 3
|
||||
run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
|
||||
|
||||
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
|
||||
fix cor all filter/corotate m 1.0
|
||||
|
||||
@ -1,240 +0,0 @@
|
||||
LAMMPS (10 Mar 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units real
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long 8 10
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.bpti
|
||||
orthogonal box = (-10 -10 -30) to (50 50 30)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
892 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
18 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
906 bonds
|
||||
reading angles ...
|
||||
1626 angles
|
||||
reading dihedrals ...
|
||||
2501 dihedrals
|
||||
reading impropers ...
|
||||
137 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
9 = max # of 1-3 neighbors
|
||||
19 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
|
||||
special_bonds charmm
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
|
||||
# ------------- MINIMIZE ----------
|
||||
|
||||
minimize 1e-4 1e-6 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.203272
|
||||
grid = 16 16 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0316399
|
||||
estimated relative force accuracy = 9.52826e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 9261 4096
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory usage (min/avg/max) = 17.8596/1/0 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -3075.6498 943.91164 -2131.7381 -380.67776
|
||||
241 0 -4503.313 749.58662 -3753.7264 -29.045104
|
||||
Loop time of 3.35722 on 1 procs for 241 steps with 892 atoms
|
||||
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2131.73812515 -3753.43984087 -3753.72636847
|
||||
Force two-norm initial, final = 1086.21 26.3688
|
||||
Force max component initial, final = 310.811 3.92748
|
||||
Final line search alpha, max atom move = 0.00596649 0.0234333
|
||||
Iterations, force evaluations = 241 463
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5003 | 2.5003 | 2.5003 | 0.0 | 74.48
|
||||
Bond | 0.24287 | 0.24287 | 0.24287 | 0.0 | 7.23
|
||||
Kspace | 0.53428 | 0.53428 | 0.53428 | 0.0 | 15.91
|
||||
Neigh | 0.069765 | 0.069765 | 0.069765 | 0.0 | 2.08
|
||||
Comm | 0.00065374 | 0.00065374 | 0.00065374 | 0.0 | 0.02
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.009358 | | | 0.28
|
||||
|
||||
Nlocal: 892 ave 892 max 892 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 31 ave 31 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 148891 ave 148891 max 148891 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 148891
|
||||
Ave neighs/atom = 166.918
|
||||
Ave special neighs/atom = 10.9395
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
# ------------- RUN ---------------
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 pair 2 kspace 3
|
||||
Respa levels:
|
||||
1 = bond angle dihedral improper
|
||||
2 = pair
|
||||
3 = kspace
|
||||
|
||||
velocity all create 200.0 12345678 dist uniform
|
||||
#dump dump1 all atom 100 4pti.dump
|
||||
|
||||
fix 1 all nvt temp 200 300 25
|
||||
fix cor all filter/corotate m 1.0
|
||||
163 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
25 = # of size 4 clusters
|
||||
0 = # of size 5 clusters
|
||||
100 = # of frozen angles
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.203272
|
||||
grid = 16 16 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0316399
|
||||
estimated relative force accuracy = 9.52826e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 9261 4096
|
||||
Per MPI rank memory usage (min/avg/max) = 19.5425/1/0 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
|
||||
PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592
|
||||
E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
|
||||
E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283
|
||||
---------------- Step 100 ----- CPU = 3.9414 (sec) ----------------
|
||||
TotEng = -2718.8970 KinEng = 538.6206 Temp = 202.8014
|
||||
PotEng = -3257.5176 E_bond = 203.3367 E_angle = 566.5317
|
||||
E_dihed = 397.6202 E_impro = 34.6623 E_vdwl = -248.7451
|
||||
E_coul = -874.5122 E_long = -3336.4111 Press = 135.8662
|
||||
---------------- Step 200 ----- CPU = 7.9028 (sec) ----------------
|
||||
TotEng = -2660.1406 KinEng = 626.3319 Temp = 235.8265
|
||||
PotEng = -3286.4725 E_bond = 209.5147 E_angle = 591.7773
|
||||
E_dihed = 388.9591 E_impro = 29.4992 E_vdwl = -243.5808
|
||||
E_coul = -923.5115 E_long = -3339.1306 Press = 88.9000
|
||||
---------------- Step 300 ----- CPU = 11.8246 (sec) ----------------
|
||||
TotEng = -2673.8090 KinEng = 616.7924 Temp = 232.2346
|
||||
PotEng = -3290.6014 E_bond = 202.8254 E_angle = 568.6860
|
||||
E_dihed = 378.4182 E_impro = 38.2399 E_vdwl = -221.3236
|
||||
E_coul = -915.3004 E_long = -3342.1468 Press = 78.8527
|
||||
---------------- Step 400 ----- CPU = 15.7990 (sec) ----------------
|
||||
TotEng = -2614.9416 KinEng = 649.3474 Temp = 244.4922
|
||||
PotEng = -3264.2890 E_bond = 211.6116 E_angle = 617.2026
|
||||
E_dihed = 399.8744 E_impro = 40.2678 E_vdwl = -211.7790
|
||||
E_coul = -978.1624 E_long = -3343.3041 Press = -4.1958
|
||||
---------------- Step 500 ----- CPU = 19.8146 (sec) ----------------
|
||||
TotEng = -2588.6772 KinEng = 660.1424 Temp = 248.5568
|
||||
PotEng = -3248.8196 E_bond = 218.4786 E_angle = 620.8605
|
||||
E_dihed = 390.3220 E_impro = 41.6794 E_vdwl = -226.3657
|
||||
E_coul = -953.1676 E_long = -3340.6269 Press = 99.3200
|
||||
---------------- Step 600 ----- CPU = 23.8587 (sec) ----------------
|
||||
TotEng = -2550.4618 KinEng = 693.3384 Temp = 261.0557
|
||||
PotEng = -3243.8002 E_bond = 232.3563 E_angle = 606.2922
|
||||
E_dihed = 396.2469 E_impro = 37.1980 E_vdwl = -235.8425
|
||||
E_coul = -937.1208 E_long = -3342.9303 Press = -21.7737
|
||||
---------------- Step 700 ----- CPU = 27.8381 (sec) ----------------
|
||||
TotEng = -2554.4355 KinEng = 692.8951 Temp = 260.8888
|
||||
PotEng = -3247.3306 E_bond = 216.3395 E_angle = 637.7785
|
||||
E_dihed = 391.5940 E_impro = 43.1426 E_vdwl = -187.6159
|
||||
E_coul = -1008.1694 E_long = -3340.3998 Press = 75.1484
|
||||
---------------- Step 800 ----- CPU = 31.8039 (sec) ----------------
|
||||
TotEng = -2508.3551 KinEng = 699.0766 Temp = 263.2163
|
||||
PotEng = -3207.4317 E_bond = 241.9936 E_angle = 641.3631
|
||||
E_dihed = 386.2198 E_impro = 43.7793 E_vdwl = -217.7523
|
||||
E_coul = -964.6070 E_long = -3338.4282 Press = -127.7337
|
||||
---------------- Step 900 ----- CPU = 35.7700 (sec) ----------------
|
||||
TotEng = -2452.7644 KinEng = 762.1842 Temp = 286.9776
|
||||
PotEng = -3214.9485 E_bond = 243.9191 E_angle = 649.8664
|
||||
E_dihed = 382.4351 E_impro = 39.0029 E_vdwl = -221.3389
|
||||
E_coul = -970.8965 E_long = -3337.9366 Press = 122.7720
|
||||
---------------- Step 1000 ----- CPU = 39.7695 (sec) ----------------
|
||||
TotEng = -2386.6805 KinEng = 799.0253 Temp = 300.8490
|
||||
PotEng = -3185.7058 E_bond = 265.3649 E_angle = 661.7543
|
||||
E_dihed = 374.6843 E_impro = 38.6877 E_vdwl = -229.2030
|
||||
E_coul = -960.7041 E_long = -3336.2899 Press = -17.9910
|
||||
Loop time of 39.7695 on 1 procs for 1000 steps with 892 atoms
|
||||
|
||||
Performance: 17.380 ns/day, 1.381 hours/ns, 25.145 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 | 29.169 | 29.169 | 29.169 | 0.0 | 73.34
|
||||
Bond | 7.6249 | 7.6249 | 7.6249 | 0.0 | 19.17
|
||||
Kspace | 1.1525 | 1.1525 | 1.1525 | 0.0 | 2.90
|
||||
Neigh | 0.87606 | 0.87606 | 0.87606 | 0.0 | 2.20
|
||||
Comm | 0.01563 | 0.01563 | 0.01563 | 0.0 | 0.04
|
||||
Output | 0.00048423 | 0.00048423 | 0.00048423 | 0.0 | 0.00
|
||||
Modify | 0.80446 | 0.80446 | 0.80446 | 0.0 | 2.02
|
||||
Other | | 0.1266 | | | 0.32
|
||||
|
||||
Nlocal: 892 ave 892 max 892 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 27 ave 27 max 27 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 146206 ave 146206 max 146206 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 146206
|
||||
Ave neighs/atom = 163.908
|
||||
Ave special neighs/atom = 10.9395
|
||||
Neighbor list builds = 186
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix cor
|
||||
unfix 1
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:43
|
||||
@ -1,240 +0,0 @@
|
||||
LAMMPS (10 Mar 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units real
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long 8 10
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.bpti
|
||||
orthogonal box = (-10 -10 -30) to (50 50 30)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
892 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
18 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
906 bonds
|
||||
reading angles ...
|
||||
1626 angles
|
||||
reading dihedrals ...
|
||||
2501 dihedrals
|
||||
reading impropers ...
|
||||
137 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
9 = max # of 1-3 neighbors
|
||||
19 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
|
||||
special_bonds charmm
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
|
||||
# ------------- MINIMIZE ----------
|
||||
|
||||
minimize 1e-4 1e-6 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.203272
|
||||
grid = 16 16 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0316399
|
||||
estimated relative force accuracy = 9.52826e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3549 1024
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory usage (min/avg/max) = 16.9693/0.981879/0 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -3075.6498 943.91164 -2131.7381 -380.67776
|
||||
241 0 -4503.3131 749.58666 -3753.7264 -29.045153
|
||||
Loop time of 1.26594 on 4 procs for 241 steps with 892 atoms
|
||||
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2131.73812515 -3753.43983927 -3753.72640137
|
||||
Force two-norm initial, final = 1086.21 26.3688
|
||||
Force max component initial, final = 310.811 3.92751
|
||||
Final line search alpha, max atom move = 0.00596649 0.0234334
|
||||
Iterations, force evaluations = 241 463
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.34267 | 0.63792 | 0.90268 | 25.2 | 50.39
|
||||
Bond | 0.025776 | 0.063318 | 0.095631 | 10.8 | 5.00
|
||||
Kspace | 0.21904 | 0.51601 | 0.84895 | 31.3 | 40.76
|
||||
Neigh | 0.023185 | 0.023363 | 0.023538 | 0.1 | 1.85
|
||||
Comm | 0.012025 | 0.014189 | 0.016335 | 1.4 | 1.12
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01114 | | | 0.88
|
||||
|
||||
Nlocal: 223 ave 323 max 89 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 613 ave 675 max 557 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 37222.8 ave 50005 max 20830 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 148891
|
||||
Ave neighs/atom = 166.918
|
||||
Ave special neighs/atom = 10.9395
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
# ------------- RUN ---------------
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 pair 2 kspace 3
|
||||
Respa levels:
|
||||
1 = bond angle dihedral improper
|
||||
2 = pair
|
||||
3 = kspace
|
||||
|
||||
velocity all create 200.0 12345678 dist uniform
|
||||
#dump dump1 all atom 100 4pti.dump
|
||||
|
||||
fix 1 all nvt temp 200 300 25
|
||||
fix cor all filter/corotate m 1.0
|
||||
163 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
25 = # of size 4 clusters
|
||||
0 = # of size 5 clusters
|
||||
100 = # of frozen angles
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.203272
|
||||
grid = 16 16 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0316399
|
||||
estimated relative force accuracy = 9.52826e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3549 1024
|
||||
Per MPI rank memory usage (min/avg/max) = 17.142/0.97212/0 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
|
||||
PotEng = -3751.5182 E_bond = 42.2810 E_angle = 345.2592
|
||||
E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
|
||||
E_coul = -886.3622 E_long = -3326.2088 Press = 83.2282
|
||||
---------------- Step 100 ----- CPU = 1.5457 (sec) ----------------
|
||||
TotEng = -2718.9184 KinEng = 538.6205 Temp = 202.8014
|
||||
PotEng = -3257.5389 E_bond = 203.3365 E_angle = 566.5311
|
||||
E_dihed = 397.6202 E_impro = 34.6621 E_vdwl = -248.7451
|
||||
E_coul = -874.5326 E_long = -3336.4111 Press = 135.8435
|
||||
---------------- Step 200 ----- CPU = 3.0720 (sec) ----------------
|
||||
TotEng = -2660.1146 KinEng = 626.3474 Temp = 235.8323
|
||||
PotEng = -3286.4620 E_bond = 209.5168 E_angle = 591.7735
|
||||
E_dihed = 388.9615 E_impro = 29.5000 E_vdwl = -243.5840
|
||||
E_coul = -923.4998 E_long = -3339.1299 Press = 88.8857
|
||||
---------------- Step 300 ----- CPU = 4.5597 (sec) ----------------
|
||||
TotEng = -2669.7442 KinEng = 619.3625 Temp = 233.2023
|
||||
PotEng = -3289.1067 E_bond = 203.4405 E_angle = 569.5281
|
||||
E_dihed = 378.3314 E_impro = 38.2880 E_vdwl = -221.1904
|
||||
E_coul = -915.3396 E_long = -3342.1646 Press = 79.3780
|
||||
---------------- Step 400 ----- CPU = 5.9808 (sec) ----------------
|
||||
TotEng = -2618.9975 KinEng = 644.6145 Temp = 242.7102
|
||||
PotEng = -3263.6119 E_bond = 209.5864 E_angle = 618.8954
|
||||
E_dihed = 401.3798 E_impro = 39.9064 E_vdwl = -212.1271
|
||||
E_coul = -977.1589 E_long = -3344.0940 Press = -7.8938
|
||||
---------------- Step 500 ----- CPU = 7.4159 (sec) ----------------
|
||||
TotEng = -2579.7486 KinEng = 666.4643 Temp = 250.9371
|
||||
PotEng = -3246.2129 E_bond = 219.2549 E_angle = 620.3474
|
||||
E_dihed = 388.4395 E_impro = 41.4499 E_vdwl = -225.9686
|
||||
E_coul = -949.3689 E_long = -3340.3672 Press = 113.2543
|
||||
---------------- Step 600 ----- CPU = 8.9252 (sec) ----------------
|
||||
TotEng = -2535.8235 KinEng = 708.5919 Temp = 266.7990
|
||||
PotEng = -3244.4154 E_bond = 243.9451 E_angle = 606.0866
|
||||
E_dihed = 400.0562 E_impro = 33.9708 E_vdwl = -223.1319
|
||||
E_coul = -964.9940 E_long = -3340.3482 Press = -102.4475
|
||||
---------------- Step 700 ----- CPU = 10.4022 (sec) ----------------
|
||||
TotEng = -2552.6681 KinEng = 702.3080 Temp = 264.4330
|
||||
PotEng = -3254.9761 E_bond = 250.8834 E_angle = 639.0977
|
||||
E_dihed = 386.4014 E_impro = 42.3004 E_vdwl = -224.4816
|
||||
E_coul = -1011.8551 E_long = -3337.3222 Press = 10.6424
|
||||
---------------- Step 800 ----- CPU = 11.8699 (sec) ----------------
|
||||
TotEng = -2423.5415 KinEng = 772.1254 Temp = 290.7206
|
||||
PotEng = -3195.6670 E_bond = 238.5831 E_angle = 640.9180
|
||||
E_dihed = 377.7994 E_impro = 40.3135 E_vdwl = -216.5705
|
||||
E_coul = -935.1087 E_long = -3341.6019 Press = -38.2479
|
||||
---------------- Step 900 ----- CPU = 13.3548 (sec) ----------------
|
||||
TotEng = -2394.4779 KinEng = 766.6895 Temp = 288.6739
|
||||
PotEng = -3161.1673 E_bond = 284.8428 E_angle = 671.0959
|
||||
E_dihed = 380.3406 E_impro = 51.2975 E_vdwl = -219.5211
|
||||
E_coul = -990.6305 E_long = -3338.5925 Press = -15.2279
|
||||
---------------- Step 1000 ----- CPU = 14.7908 (sec) ----------------
|
||||
TotEng = -2340.1471 KinEng = 799.0198 Temp = 300.8469
|
||||
PotEng = -3139.1669 E_bond = 271.0389 E_angle = 683.8278
|
||||
E_dihed = 407.0795 E_impro = 39.6209 E_vdwl = -230.5355
|
||||
E_coul = -974.2981 E_long = -3335.9003 Press = -94.3420
|
||||
Loop time of 14.7909 on 4 procs for 1000 steps with 892 atoms
|
||||
|
||||
Performance: 46.732 ns/day, 0.514 hours/ns, 67.609 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.4184 | 7.5543 | 10.133 | 74.2 | 51.07
|
||||
Bond | 0.94027 | 1.9781 | 2.7492 | 54.4 | 13.37
|
||||
Kspace | 0.45487 | 0.45887 | 0.46343 | 0.4 | 3.10
|
||||
Neigh | 0.28145 | 0.28339 | 0.28539 | 0.3 | 1.92
|
||||
Comm | 0.7515 | 4.1484 | 8.3861 | 135.5 | 28.05
|
||||
Output | 0.00049973 | 0.00055474 | 0.00066924 | 0.0 | 0.00
|
||||
Modify | 0.26165 | 0.31142 | 0.35023 | 6.7 | 2.11
|
||||
Other | | 0.05572 | | | 0.38
|
||||
|
||||
Nlocal: 223 ave 313 max 122 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Nghost: 584.5 ave 605 max 553 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 35448 ave 42093 max 25175 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 141792
|
||||
Ave neighs/atom = 158.96
|
||||
Ave special neighs/atom = 10.9395
|
||||
Neighbor list builds = 186
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix cor
|
||||
unfix 1
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:16
|
||||
@ -1,146 +0,0 @@
|
||||
LAMMPS (10 Mar 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide, run for 8ps in NVT
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
thermo 50
|
||||
#dump dump1 all atom 100 peptide.dump
|
||||
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 pair 2 kspace 3
|
||||
Respa levels:
|
||||
1 = bond angle dihedral improper
|
||||
2 = pair
|
||||
3 = kspace
|
||||
|
||||
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
|
||||
fix cor all filter/corotate m 1.0
|
||||
19 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
0 = # of size 5 clusters
|
||||
646 = # of frozen angles
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory usage (min/avg/max) = 22.6706/1/0 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821
|
||||
50 239.46028 -7546.5667 1092.8874 -5023.9668 -24643.891
|
||||
100 242.81799 -7125.5527 416.0788 -5259.7139 15525.465
|
||||
150 235.97108 -7531.9334 932.35464 -5190.6987 -14838.489
|
||||
200 252.06415 -7195.6011 568.02993 -5122.6064 8841.332
|
||||
250 249.99431 -7586.5092 881.83491 -5212.0676 -9330.345
|
||||
300 240.3382 -7333.0933 633.29951 -5264.8395 5137.9757
|
||||
350 255.34529 -7568.2413 856.46371 -5187.2226 -6206.063
|
||||
400 242.99276 -7419.9031 713.23943 -5255.8602 2447.0091
|
||||
450 251.10653 -7622.061 844.20584 -5278.6079 -4906.6559
|
||||
500 255.59314 -7439.253 710.84907 -5202.3691 1571.0032
|
||||
550 253.2025 -7660.5101 823.05373 -5325.695 -4551.399
|
||||
600 249.05313 -7509.6729 741.48104 -5281.2046 992.87
|
||||
650 251.75984 -7593.6589 847.08244 -5243.4286 -3510.1176
|
||||
700 249.25027 -7601.9112 794.0912 -5319.6557 305.76021
|
||||
750 255.415 -7602.2674 822.98524 -5254.3109 -2333.421
|
||||
800 241.99621 -7643.8878 796.53352 -5402.5008 -298.66565
|
||||
850 253.6428 -7598.3764 816.45457 -5267.5316 -1905.3478
|
||||
900 247.20231 -7690.2806 789.75999 -5424.5838 -1331.7228
|
||||
950 255.92583 -7634.7505 831.18272 -5275.5466 -2186.5117
|
||||
1000 253.2126 -7647.9526 823.93602 -5312.195 -1189.9659
|
||||
Loop time of 150.664 on 1 procs for 1000 steps with 2004 atoms
|
||||
|
||||
Performance: 4.588 ns/day, 5.231 hours/ns, 6.637 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 135.81 | 135.81 | 135.81 | 0.0 | 90.14
|
||||
Bond | 2.5889 | 2.5889 | 2.5889 | 0.0 | 1.72
|
||||
Kspace | 2.0379 | 2.0379 | 2.0379 | 0.0 | 1.35
|
||||
Neigh | 5.893 | 5.893 | 5.893 | 0.0 | 3.91
|
||||
Comm | 1.6998 | 1.6998 | 1.6998 | 0.0 | 1.13
|
||||
Output | 0.00077915 | 0.00077915 | 0.00077915 | 0.0 | 0.00
|
||||
Modify | 2 | 2 | 2 | 0.0 | 1.33
|
||||
Other | | 0.6352 | | | 0.42
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11197 ave 11197 max 11197 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 707779 ave 707779 max 707779 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 707779
|
||||
Ave neighs/atom = 353.183
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds = 200
|
||||
unfix cor
|
||||
unfix 1
|
||||
|
||||
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:02:30
|
||||
@ -1,146 +0,0 @@
|
||||
LAMMPS (10 Mar 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide, run for 8ps in NVT
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
thermo 50
|
||||
#dump dump1 all atom 100 peptide.dump
|
||||
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 pair 2 kspace 3
|
||||
Respa levels:
|
||||
1 = bond angle dihedral improper
|
||||
2 = pair
|
||||
3 = kspace
|
||||
|
||||
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
|
||||
fix cor all filter/corotate m 1.0
|
||||
19 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
0 = # of size 5 clusters
|
||||
646 = # of frozen angles
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory usage (min/avg/max) = 16.8394/0.98826/0 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821
|
||||
50 239.46028 -7546.5668 1092.8874 -5023.9668 -24643.891
|
||||
100 242.81819 -7125.5629 416.08082 -5259.7209 15525.244
|
||||
150 235.94928 -7531.9186 932.50658 -5190.6621 -14842.431
|
||||
200 255.85551 -7254.4065 568.8803 -5157.9249 8936.8651
|
||||
250 247.8705 -7607.4583 858.06087 -5269.4711 -9926.0442
|
||||
300 257.64176 -7267.424 618.5573 -5110.6004 5173.3307
|
||||
350 251.65439 -7572.3806 821.15745 -5248.7049 -7092.327
|
||||
400 256.87927 -7414.2145 655.33178 -5225.169 4119.4095
|
||||
450 257.12393 -7576.5541 853.39773 -5187.9819 -5224.8823
|
||||
500 242.42371 -7524.705 705.75357 -5371.5455 2111.3878
|
||||
550 248.97188 -7541.076 792.86994 -5261.7038 -2278.4185
|
||||
600 249.81862 -7592.0499 767.17722 -5333.3149 -1149.4759
|
||||
650 253.31349 -7578.2665 813.75975 -5252.0827 -2915.5706
|
||||
700 256.61152 -7588.1475 761.03356 -5294.9988 -747.88089
|
||||
750 248.3606 -7660.457 837.71615 -5339.8883 -3072.8311
|
||||
800 253.81464 -7638.6089 782.4229 -5340.7698 -1025.909
|
||||
850 245.69185 -7660.9036 795.66792 -5398.3172 -2717.5851
|
||||
900 249.13156 -7589.4769 806.43464 -5295.5867 -761.63361
|
||||
950 251.11482 -7691.4981 869.34937 -5322.852 -3282.3031
|
||||
1000 241.9195 -7630.9899 828.59107 -5358.0033 -95.962685
|
||||
Loop time of 45.5507 on 4 procs for 1000 steps with 2004 atoms
|
||||
|
||||
Performance: 15.174 ns/day, 1.582 hours/ns, 21.954 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 35.545 | 36.674 | 38.004 | 15.8 | 80.51
|
||||
Bond | 0.51302 | 0.67796 | 0.86345 | 18.6 | 1.49
|
||||
Kspace | 0.66031 | 0.68459 | 0.70506 | 2.1 | 1.50
|
||||
Neigh | 1.5605 | 1.5627 | 1.5649 | 0.1 | 3.43
|
||||
Comm | 3.4611 | 4.9841 | 6.294 | 47.2 | 10.94
|
||||
Output | 0.00079799 | 0.00086641 | 0.0010369 | 0.0 | 0.00
|
||||
Modify | 0.67341 | 0.69059 | 0.71186 | 1.7 | 1.52
|
||||
Other | | 0.2762 | | | 0.61
|
||||
|
||||
Nlocal: 501 ave 523 max 473 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Nghost: 6643.25 ave 6708 max 6566 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 176977 ave 185765 max 164931 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 707908
|
||||
Ave neighs/atom = 353.248
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds = 200
|
||||
unfix cor
|
||||
unfix 1
|
||||
|
||||
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:45
|
||||
241
examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1
Normal file
241
examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1
Normal file
@ -0,0 +1,241 @@
|
||||
LAMMPS (20 Jun 2017)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units real
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long 8 10
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.bpti
|
||||
orthogonal box = (-10 -10 -30) to (50 50 30)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
892 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
18 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
906 bonds
|
||||
reading angles ...
|
||||
1626 angles
|
||||
reading dihedrals ...
|
||||
2501 dihedrals
|
||||
reading impropers ...
|
||||
137 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
9 = max # of 1-3 neighbors
|
||||
19 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
|
||||
special_bonds charmm
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
|
||||
# ------------- MINIMIZE ----------
|
||||
|
||||
minimize 1e-4 1e-6 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.203272
|
||||
grid = 16 16 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0316399
|
||||
estimated relative force accuracy = 9.52826e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 9261 4096
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/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) = 17.86 | 17.86 | 17.86 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -3075.6498 943.91164 -2131.7381 -380.67776
|
||||
241 0 -4503.313 749.58662 -3753.7264 -29.045104
|
||||
Loop time of 7.63279 on 1 procs for 241 steps with 892 atoms
|
||||
|
||||
32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2131.73812515 -3753.43984087 -3753.72636847
|
||||
Force two-norm initial, final = 1086.21 26.3688
|
||||
Force max component initial, final = 310.811 3.92748
|
||||
Final line search alpha, max atom move = 0.00596649 0.0234333
|
||||
Iterations, force evaluations = 241 463
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.8395 | 5.8395 | 5.8395 | 0.0 | 76.51
|
||||
Bond | 0.46414 | 0.46414 | 0.46414 | 0.0 | 6.08
|
||||
Kspace | 1.1535 | 1.1535 | 1.1535 | 0.0 | 15.11
|
||||
Neigh | 0.14908 | 0.14908 | 0.14908 | 0.0 | 1.95
|
||||
Comm | 0.001932 | 0.001932 | 0.001932 | 0.0 | 0.03
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.02465 | | | 0.32
|
||||
|
||||
Nlocal: 892 ave 892 max 892 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 31 ave 31 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 148891 ave 148891 max 148891 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 148891
|
||||
Ave neighs/atom = 166.918
|
||||
Ave special neighs/atom = 10.9395
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
# ------------- RUN ---------------
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
|
||||
Respa levels:
|
||||
1 = bond angle
|
||||
2 = dihedral improper pair
|
||||
3 = kspace
|
||||
|
||||
velocity all create 200.0 12345678 dist uniform
|
||||
#dump dump1 all atom 100 4pti.dump
|
||||
|
||||
fix 1 all nvt temp 200 300 25
|
||||
fix cor all filter/corotate m 1.0
|
||||
163 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
25 = # of size 4 clusters
|
||||
0 = # of size 5 clusters
|
||||
100 = # of frozen angles
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.203272
|
||||
grid = 16 16 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0316399
|
||||
estimated relative force accuracy = 9.52826e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 9261 4096
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.55 | 19.55 | 19.55 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
|
||||
PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592
|
||||
E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
|
||||
E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283
|
||||
---------------- Step 100 ----- CPU = 8.4380 (sec) ----------------
|
||||
TotEng = -2718.4258 KinEng = 539.6265 Temp = 203.1802
|
||||
PotEng = -3258.0524 E_bond = 203.2307 E_angle = 566.1893
|
||||
E_dihed = 397.6759 E_impro = 34.7696 E_vdwl = -248.6577
|
||||
E_coul = -874.8466 E_long = -3336.4135 Press = 135.8640
|
||||
---------------- Step 200 ----- CPU = 16.9012 (sec) ----------------
|
||||
TotEng = -2661.9611 KinEng = 625.0674 Temp = 235.3503
|
||||
PotEng = -3287.0285 E_bond = 208.1804 E_angle = 590.8462
|
||||
E_dihed = 389.1482 E_impro = 30.5882 E_vdwl = -240.5448
|
||||
E_coul = -926.3091 E_long = -3338.9378 Press = 103.4738
|
||||
---------------- Step 300 ----- CPU = 25.3046 (sec) ----------------
|
||||
TotEng = -2662.4139 KinEng = 622.2647 Temp = 234.2951
|
||||
PotEng = -3284.6785 E_bond = 202.4210 E_angle = 573.6793
|
||||
E_dihed = 382.8919 E_impro = 41.8973 E_vdwl = -218.9895
|
||||
E_coul = -924.8414 E_long = -3341.7372 Press = 40.6746
|
||||
---------------- Step 400 ----- CPU = 33.8063 (sec) ----------------
|
||||
TotEng = -2604.9431 KinEng = 662.9890 Temp = 249.6286
|
||||
PotEng = -3267.9321 E_bond = 195.9116 E_angle = 616.1383
|
||||
E_dihed = 407.8502 E_impro = 43.3560 E_vdwl = -219.0377
|
||||
E_coul = -966.3118 E_long = -3345.8387 Press = -91.8856
|
||||
---------------- Step 500 ----- CPU = 42.3470 (sec) ----------------
|
||||
TotEng = -2609.3867 KinEng = 657.0939 Temp = 247.4090
|
||||
PotEng = -3266.4806 E_bond = 236.4955 E_angle = 570.6256
|
||||
E_dihed = 390.5111 E_impro = 41.9250 E_vdwl = -223.9927
|
||||
E_coul = -939.5249 E_long = -3342.5201 Press = 236.7471
|
||||
---------------- Step 600 ----- CPU = 50.9590 (sec) ----------------
|
||||
TotEng = -2564.7161 KinEng = 701.8494 Temp = 264.2603
|
||||
PotEng = -3266.5655 E_bond = 223.5820 E_angle = 582.7722
|
||||
E_dihed = 394.6196 E_impro = 43.8581 E_vdwl = -201.7759
|
||||
E_coul = -967.4136 E_long = -3342.2079 Press = 26.6595
|
||||
---------------- Step 700 ----- CPU = 59.4791 (sec) ----------------
|
||||
TotEng = -2510.1142 KinEng = 689.5931 Temp = 259.6455
|
||||
PotEng = -3199.7072 E_bond = 254.6476 E_angle = 611.9715
|
||||
E_dihed = 403.0624 E_impro = 44.1360 E_vdwl = -205.6377
|
||||
E_coul = -964.7455 E_long = -3343.1416 Press = 60.5789
|
||||
---------------- Step 800 ----- CPU = 67.9330 (sec) ----------------
|
||||
TotEng = -2452.7408 KinEng = 777.5962 Temp = 292.7805
|
||||
PotEng = -3230.3370 E_bond = 250.4950 E_angle = 656.6738
|
||||
E_dihed = 382.4702 E_impro = 39.5378 E_vdwl = -225.0375
|
||||
E_coul = -994.4519 E_long = -3340.0244 Press = -19.6463
|
||||
---------------- Step 900 ----- CPU = 76.3690 (sec) ----------------
|
||||
TotEng = -2339.9766 KinEng = 808.7116 Temp = 304.4961
|
||||
PotEng = -3148.6883 E_bond = 247.7657 E_angle = 679.0658
|
||||
E_dihed = 398.2984 E_impro = 43.7890 E_vdwl = -230.2498
|
||||
E_coul = -945.8152 E_long = -3341.5422 Press = -64.4343
|
||||
---------------- Step 1000 ----- CPU = 84.8757 (sec) ----------------
|
||||
TotEng = -2329.1819 KinEng = 822.9820 Temp = 309.8691
|
||||
PotEng = -3152.1639 E_bond = 264.9609 E_angle = 691.7104
|
||||
E_dihed = 385.9914 E_impro = 40.5525 E_vdwl = -230.5182
|
||||
E_coul = -954.6203 E_long = -3350.2405 Press = -146.6649
|
||||
Loop time of 84.8758 on 1 procs for 1000 steps with 892 atoms
|
||||
|
||||
Performance: 8.144 ns/day, 2.947 hours/ns, 11.782 timesteps/s
|
||||
32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 68.548 | 68.548 | 68.548 | 0.0 | 80.76
|
||||
Bond | 10.263 | 10.263 | 10.263 | 0.0 | 12.09
|
||||
Kspace | 2.4528 | 2.4528 | 2.4528 | 0.0 | 2.89
|
||||
Neigh | 1.9041 | 1.9041 | 1.9041 | 0.0 | 2.24
|
||||
Comm | 0.044126 | 0.044126 | 0.044126 | 0.0 | 0.05
|
||||
Output | 0.000983 | 0.000983 | 0.000983 | 0.0 | 0.00
|
||||
Modify | 1.4113 | 1.4113 | 1.4113 | 0.0 | 1.66
|
||||
Other | | 0.2516 | | | 0.30
|
||||
|
||||
Nlocal: 892 ave 892 max 892 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 38 ave 38 max 38 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 144068 ave 144068 max 144068 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 144068
|
||||
Ave neighs/atom = 161.511
|
||||
Ave special neighs/atom = 10.9395
|
||||
Neighbor list builds = 190
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix cor
|
||||
unfix 1
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:32
|
||||
241
examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4
Normal file
241
examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4
Normal file
@ -0,0 +1,241 @@
|
||||
LAMMPS (20 Jun 2017)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units real
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
|
||||
pair_style lj/charmm/coul/long 8 10
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data data.bpti
|
||||
orthogonal box = (-10 -10 -30) to (50 50 30)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
892 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
18 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
2 = max impropers/atom
|
||||
reading bonds ...
|
||||
906 bonds
|
||||
reading angles ...
|
||||
1626 angles
|
||||
reading dihedrals ...
|
||||
2501 dihedrals
|
||||
reading impropers ...
|
||||
137 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
9 = max # of 1-3 neighbors
|
||||
19 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
|
||||
special_bonds charmm
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
|
||||
# ------------- MINIMIZE ----------
|
||||
|
||||
minimize 1e-4 1e-6 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.203272
|
||||
grid = 16 16 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0316399
|
||||
estimated relative force accuracy = 9.52826e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3549 1024
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/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) = 16.97 | 17.2 | 17.52 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -3075.6498 943.91164 -2131.7381 -380.67776
|
||||
241 0 -4503.3131 749.58665 -3753.7264 -29.044989
|
||||
Loop time of 3.06327 on 4 procs for 241 steps with 892 atoms
|
||||
|
||||
31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2131.73812515 -3753.4398752 -3753.72640446
|
||||
Force two-norm initial, final = 1086.21 26.3687
|
||||
Force max component initial, final = 310.811 3.92765
|
||||
Final line search alpha, max atom move = 0.0059665 0.0234343
|
||||
Iterations, force evaluations = 241 463
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.91458 | 1.6235 | 2.2701 | 38.2 | 53.00
|
||||
Bond | 0.055164 | 0.13173 | 0.19487 | 15.1 | 4.30
|
||||
Kspace | 0.48966 | 1.1993 | 1.9847 | 48.7 | 39.15
|
||||
Neigh | 0.053297 | 0.053442 | 0.053576 | 0.0 | 1.74
|
||||
Comm | 0.031677 | 0.035006 | 0.038061 | 1.5 | 1.14
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.02021 | | | 0.66
|
||||
|
||||
Nlocal: 223 ave 323 max 89 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 613 ave 675 max 557 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 37222.8 ave 50005 max 20830 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 148891
|
||||
Ave neighs/atom = 166.918
|
||||
Ave special neighs/atom = 10.9395
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
# ------------- RUN ---------------
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
|
||||
Respa levels:
|
||||
1 = bond angle
|
||||
2 = dihedral improper pair
|
||||
3 = kspace
|
||||
|
||||
velocity all create 200.0 12345678 dist uniform
|
||||
#dump dump1 all atom 100 4pti.dump
|
||||
|
||||
fix 1 all nvt temp 200 300 25
|
||||
fix cor all filter/corotate m 1.0
|
||||
163 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
25 = # of size 4 clusters
|
||||
0 = # of size 5 clusters
|
||||
100 = # of frozen angles
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.203272
|
||||
grid = 16 16 16
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0316399
|
||||
estimated relative force accuracy = 9.52826e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 3549 1024
|
||||
Per MPI rank memory allocation (min/avg/max) = 17.14 | 17.63 | 18.14 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
|
||||
PotEng = -3751.5182 E_bond = 42.2810 E_angle = 345.2593
|
||||
E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
|
||||
E_coul = -886.3622 E_long = -3326.2088 Press = 83.2284
|
||||
---------------- Step 100 ----- CPU = 3.4639 (sec) ----------------
|
||||
TotEng = -2718.4266 KinEng = 539.6246 Temp = 203.1794
|
||||
PotEng = -3258.0513 E_bond = 203.2306 E_angle = 566.1887
|
||||
E_dihed = 397.6756 E_impro = 34.7695 E_vdwl = -248.6577
|
||||
E_coul = -874.8446 E_long = -3336.4135 Press = 135.8653
|
||||
---------------- Step 200 ----- CPU = 6.8898 (sec) ----------------
|
||||
TotEng = -2662.0450 KinEng = 625.0178 Temp = 235.3317
|
||||
PotEng = -3287.0628 E_bond = 208.1691 E_angle = 590.8259
|
||||
E_dihed = 389.1424 E_impro = 30.5879 E_vdwl = -240.5397
|
||||
E_coul = -926.3110 E_long = -3338.9375 Press = 103.4843
|
||||
---------------- Step 300 ----- CPU = 10.2791 (sec) ----------------
|
||||
TotEng = -2661.8829 KinEng = 623.0352 Temp = 234.5852
|
||||
PotEng = -3284.9181 E_bond = 203.0274 E_angle = 573.6583
|
||||
E_dihed = 383.0124 E_impro = 41.9015 E_vdwl = -218.0696
|
||||
E_coul = -926.5806 E_long = -3341.8675 Press = 45.6868
|
||||
---------------- Step 400 ----- CPU = 13.5874 (sec) ----------------
|
||||
TotEng = -2594.5220 KinEng = 672.8693 Temp = 253.3487
|
||||
PotEng = -3267.3914 E_bond = 201.3378 E_angle = 612.7099
|
||||
E_dihed = 410.1920 E_impro = 44.0201 E_vdwl = -217.9714
|
||||
E_coul = -971.6203 E_long = -3346.0595 Press = -121.1015
|
||||
---------------- Step 500 ----- CPU = 16.9047 (sec) ----------------
|
||||
TotEng = -2603.9306 KinEng = 668.2122 Temp = 251.5952
|
||||
PotEng = -3272.1428 E_bond = 238.1081 E_angle = 578.3310
|
||||
E_dihed = 399.1305 E_impro = 41.4314 E_vdwl = -216.9664
|
||||
E_coul = -969.4047 E_long = -3342.7729 Press = 156.7851
|
||||
---------------- Step 600 ----- CPU = 20.1970 (sec) ----------------
|
||||
TotEng = -2531.1096 KinEng = 728.1698 Temp = 274.1705
|
||||
PotEng = -3259.2794 E_bond = 232.8396 E_angle = 621.3323
|
||||
E_dihed = 398.1952 E_impro = 37.0914 E_vdwl = -241.6350
|
||||
E_coul = -963.1540 E_long = -3343.9488 Press = 58.6784
|
||||
---------------- Step 700 ----- CPU = 23.4360 (sec) ----------------
|
||||
TotEng = -2499.9495 KinEng = 742.1211 Temp = 279.4234
|
||||
PotEng = -3242.0705 E_bond = 240.5622 E_angle = 582.9270
|
||||
E_dihed = 396.6246 E_impro = 36.6510 E_vdwl = -228.4925
|
||||
E_coul = -926.8734 E_long = -3343.4695 Press = -60.7458
|
||||
---------------- Step 800 ----- CPU = 26.6709 (sec) ----------------
|
||||
TotEng = -2426.0217 KinEng = 760.1083 Temp = 286.1959
|
||||
PotEng = -3186.1300 E_bond = 266.5863 E_angle = 652.3401
|
||||
E_dihed = 380.7407 E_impro = 34.6861 E_vdwl = -225.3729
|
||||
E_coul = -953.2382 E_long = -3341.8721 Press = -57.9824
|
||||
---------------- Step 900 ----- CPU = 29.8152 (sec) ----------------
|
||||
TotEng = -2419.4636 KinEng = 780.8361 Temp = 294.0004
|
||||
PotEng = -3200.2996 E_bond = 269.3237 E_angle = 665.7171
|
||||
E_dihed = 408.3527 E_impro = 43.7811 E_vdwl = -254.0696
|
||||
E_coul = -1002.0694 E_long = -3331.3352 Press = -52.0169
|
||||
---------------- Step 1000 ----- CPU = 32.8748 (sec) ----------------
|
||||
TotEng = -2398.7244 KinEng = 811.9856 Temp = 305.7288
|
||||
PotEng = -3210.7099 E_bond = 258.2207 E_angle = 639.3671
|
||||
E_dihed = 379.3353 E_impro = 41.7602 E_vdwl = -207.2654
|
||||
E_coul = -983.9330 E_long = -3338.1948 Press = 89.4870
|
||||
Loop time of 32.8751 on 4 procs for 1000 steps with 892 atoms
|
||||
|
||||
Performance: 21.025 ns/day, 1.141 hours/ns, 30.418 timesteps/s
|
||||
31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 12.449 | 19.023 | 24.612 | 99.6 | 57.86
|
||||
Bond | 1.4547 | 2.8768 | 3.9098 | 61.4 | 8.75
|
||||
Kspace | 1.0537 | 1.0778 | 1.0992 | 2.1 | 3.28
|
||||
Neigh | 0.67542 | 0.67994 | 0.68323 | 0.3 | 2.07
|
||||
Comm | 1.8602 | 8.4515 | 16.516 | 182.9 | 25.71
|
||||
Output | 0.000839 | 0.00147 | 0.003293 | 2.7 | 0.00
|
||||
Modify | 0.56658 | 0.63186 | 0.69304 | 6.8 | 1.92
|
||||
Other | | 0.133 | | | 0.40
|
||||
|
||||
Nlocal: 223 ave 339 max 136 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 590 ave 626 max 552 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 36488.2 ave 41965 max 29054 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 145953
|
||||
Ave neighs/atom = 163.624
|
||||
Ave special neighs/atom = 10.9395
|
||||
Neighbor list builds = 189
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix cor
|
||||
unfix 1
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:36
|
||||
147
examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1
Normal file
147
examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1
Normal file
@ -0,0 +1,147 @@
|
||||
LAMMPS (20 Jun 2017)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide, run for 8ps in NVT
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
thermo 50
|
||||
#dump dump1 all atom 100 peptide.dump
|
||||
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
|
||||
Respa levels:
|
||||
1 = bond angle
|
||||
2 = dihedral improper pair
|
||||
3 = kspace
|
||||
|
||||
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
|
||||
fix cor all filter/corotate m 1.0
|
||||
19 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
0 = # of size 5 clusters
|
||||
646 = # of frozen angles
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/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) = 22.72 | 22.72 | 22.72 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984
|
||||
50 239.47667 -7205.1006 1092.7664 -4682.5237 -23733.122
|
||||
100 244.63086 -6788.0793 422.97204 -4904.5234 16458.011
|
||||
150 240.79042 -7267.0791 966.31411 -4863.1107 -13554.894
|
||||
200 254.77122 -6868.5713 591.00071 -4756.4431 10532.563
|
||||
250 241.87417 -7264.9349 856.9357 -4963.8743 -9043.4359
|
||||
300 251.37775 -6976.8 650.55612 -4825.3773 6986.2021
|
||||
350 250.81494 -7286.7011 880.11184 -4909.0829 -6392.4665
|
||||
400 247.55673 -7104.4036 701.89555 -4924.4551 4720.7811
|
||||
450 258.54988 -7215.3011 832.23692 -4839.3759 -3446.3859
|
||||
500 246.80928 -7151.2468 715.61007 -4962.0464 2637.5769
|
||||
550 246.20721 -7159.0464 805.24974 -4883.8011 -2725.227
|
||||
600 250.62483 -7201.7688 806.10076 -4899.2968 770.22352
|
||||
650 247.59777 -7260.1607 802.97277 -4978.8899 -430.42309
|
||||
700 246.86951 -7286.2971 825.99865 -4986.3486 -427.88651
|
||||
750 252.79268 -7307.8572 833.4822 -4965.0605 -614.74372
|
||||
800 251.73191 -7315.2457 839.59859 -4972.666 952.56448
|
||||
850 246.75844 -7303.6221 816.67112 -5013.6642 -2055.2823
|
||||
900 251.00123 -7317.4219 825.12165 -4993.6817 -356.53166
|
||||
950 259.20822 -7252.3466 854.62611 -4850.1016 -1719.5267
|
||||
1000 245.72486 -7347.5547 811.48146 -5068.9576 -717.6136
|
||||
Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms
|
||||
|
||||
Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s
|
||||
32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 328.2 | 328.2 | 328.2 | 0.0 | 91.80
|
||||
Bond | 4.4815 | 4.4815 | 4.4815 | 0.0 | 1.25
|
||||
Kspace | 3.9448 | 3.9448 | 3.9448 | 0.0 | 1.10
|
||||
Neigh | 12.457 | 12.457 | 12.457 | 0.0 | 3.48
|
||||
Comm | 3.2147 | 3.2147 | 3.2147 | 0.0 | 0.90
|
||||
Output | 0.001689 | 0.001689 | 0.001689 | 0.0 | 0.00
|
||||
Modify | 3.937 | 3.937 | 3.937 | 0.0 | 1.10
|
||||
Other | | 1.289 | | | 0.36
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11191 ave 11191 max 11191 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708610 ave 708610 max 708610 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708610
|
||||
Ave neighs/atom = 353.598
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds = 200
|
||||
unfix cor
|
||||
unfix 1
|
||||
|
||||
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:05:57
|
||||
147
examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4
Normal file
147
examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4
Normal file
@ -0,0 +1,147 @@
|
||||
LAMMPS (20 Jun 2017)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide, run for 8ps in NVT
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
thermo 50
|
||||
#dump dump1 all atom 100 peptide.dump
|
||||
|
||||
timestep 8
|
||||
|
||||
run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
|
||||
Respa levels:
|
||||
1 = bond angle
|
||||
2 = dihedral improper pair
|
||||
3 = kspace
|
||||
|
||||
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
|
||||
fix cor all filter/corotate m 1.0
|
||||
19 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
0 = # of size 5 clusters
|
||||
646 = # of frozen angles
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/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) = 16.87 | 17.05 | 17.26 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984
|
||||
50 239.47667 -7205.1005 1092.7664 -4682.5237 -23733.122
|
||||
100 244.63889 -6788.1152 422.96733 -4904.5161 16457.756
|
||||
150 239.36917 -7258.7053 967.87775 -4861.6589 -13526.261
|
||||
200 255.14702 -6864.0525 604.58036 -4736.1009 11013.1
|
||||
250 252.72919 -7303.0966 898.11178 -4896.0494 -8480.8766
|
||||
300 250.66477 -6989.2603 652.83649 -4839.8141 6209.3375
|
||||
350 243.30794 -7218.8575 838.31977 -4927.8525 -5180.4928
|
||||
400 256.3573 -7090.677 706.24197 -4853.8377 3302.577
|
||||
450 246.15776 -7274.574 834.31676 -4970.557 -3427.971
|
||||
500 256.28473 -7082.1447 735.42828 -4816.5524 2846.086
|
||||
550 251.32327 -7341.739 812.64934 -5028.5484 -1786.9277
|
||||
600 254.57737 -7152.3448 740.52534 -4891.8494 825.91675
|
||||
650 244.95305 -7207.1136 790.67659 -4953.9295 -520.79769
|
||||
700 249.4984 -7204.2699 779.06969 -4935.5544 -940.75384
|
||||
750 248.46962 -7232.1037 791.6642 -4956.9361 -548.12171
|
||||
800 260.2974 -7293.1982 793.23282 -4945.8435 -1171.26
|
||||
850 249.79023 -7258.3759 823.56789 -4943.4198 -499.76275
|
||||
900 249.97237 -7267.0584 784.57992 -4990.0028 -271.33531
|
||||
950 251.29018 -7261.0642 823.467 -4937.2534 -538.7168
|
||||
1000 246.05777 -7285.0948 847.90892 -4968.0826 -2613.1854
|
||||
Loop time of 94.6835 on 4 procs for 1000 steps with 2004 atoms
|
||||
|
||||
Performance: 7.300 ns/day, 3.288 hours/ns, 10.562 timesteps/s
|
||||
37.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 33.389 | 78.508 | 94.639 | 294.1 | 82.92
|
||||
Bond | 0.39957 | 1.104 | 1.4443 | 40.6 | 1.17
|
||||
Kspace | 0.53324 | 1.2631 | 1.5137 | 37.5 | 1.33
|
||||
Neigh | 1.2668 | 3.011 | 3.5942 | 58.0 | 3.18
|
||||
Comm | 3.4563 | 8.8707 | 11.494 | 107.9 | 9.37
|
||||
Output | 0.000435 | 0.0017425 | 0.004136 | 3.4 | 0.00
|
||||
Modify | 0.59335 | 1.4123 | 1.6921 | 39.8 | 1.49
|
||||
Other | | 0.5129 | | | 0.54
|
||||
|
||||
Nlocal: 501 ave 515 max 476 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 6681.5 ave 6740 max 6634 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 176872 ave 182642 max 168464 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 707486
|
||||
Ave neighs/atom = 353.037
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 200
|
||||
Dangerous builds = 200
|
||||
unfix cor
|
||||
unfix 1
|
||||
|
||||
|
||||
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:53
|
||||
@ -2,15 +2,13 @@ Run these examples as:
|
||||
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1freeend
|
||||
mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1.end
|
||||
mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac
|
||||
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1freeend
|
||||
mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac
|
||||
mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac
|
||||
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1.end
|
||||
mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.sivac
|
||||
|
||||
Note that more than 4 replicas should be used for a precise estimate
|
||||
of the activation energy corresponding to a transition.
|
||||
|
||||
@ -51,7 +51,7 @@ set group nebatoms type 3
|
||||
group nonneb subtract all nebatoms
|
||||
|
||||
fix 1 lower setforce 0.0 0.0 0.0
|
||||
fix 2 nebatoms neb 1.0 nudg_style idealpos
|
||||
fix 2 nebatoms neb 1.0 parallel ideal
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo 100
|
||||
|
||||
@ -15,7 +15,7 @@ variable u uloop 20
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
|
||||
read_data initial.hop1freeend
|
||||
read_data initial.hop1.end
|
||||
|
||||
# LJ potentials
|
||||
|
||||
@ -41,7 +41,7 @@ set group nebatoms type 3
|
||||
group nonneb subtract all nebatoms
|
||||
|
||||
fix 1 lower setforce 0.0 0.0 0.0
|
||||
fix 2 nebatoms neb 1.0 nudg_style idealpos freeend ini
|
||||
fix 2 nebatoms neb 1.0 parallel ideal end first 1.0
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo 100
|
||||
@ -65,4 +65,4 @@ thermo 100
|
||||
|
||||
min_style fire
|
||||
|
||||
neb 0.0 0.01 1000 1000 100 final final.hop2
|
||||
neb 0.0 0.05 1000 1000 100 final final.hop2
|
||||
|
||||
11
examples/neb/log.19Jun17.neb.hop1.end.g++.4
Normal file
11
examples/neb/log.19Jun17.neb.hop1.end.g++.4
Normal file
@ -0,0 +1,11 @@
|
||||
LAMMPS (19 May 2017)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928
|
||||
100 0.11027532 0.085410308 3.0967938 0.024201563 0.38551033 0.0017583261 0.0021866943 1.7710358 0 -3.0483469 0.31192818 -3.0465886 0.61093022 -3.0466143 1 -3.0487752
|
||||
130 0.09954083 0.075481108 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
130 0.37838747 0.3502435 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776
|
||||
230 0.22757286 0.12027481 3.1250243 0.0081260569 0.14019507 0.0018364585 0.002278918 1.76926 0 -3.0483347 0.39730698 -3.0464983 0.64450769 -3.0466973 1 -3.0487772
|
||||
278 0.096184498 0.085088496 3.1405655 0.0068164307 0.093861113 0.0018426056 0.002286256 1.7684765 0 -3.0483338 0.41277997 -3.0464912 0.65562984 -3.0467294 1 -3.0487775
|
||||
11
examples/neb/log.19Jun17.neb.hop1.end.g++.8
Normal file
11
examples/neb/log.19Jun17.neb.hop1.end.g++.8
Normal file
@ -0,0 +1,11 @@
|
||||
LAMMPS (19 May 2017)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928
|
||||
100 0.11375359 0.085350745 3.0966418 0.0236765 0.38531777 0.0017582606 0.0021868783 1.7710738 0 -3.0483467 0.31201141 -3.0465884 0.61117406 -3.0466149 1 -3.0487753
|
||||
119 0.09996986 0.078639268 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
119 0.3793192 0.35281863 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758
|
||||
219 0.20159133 0.12247026 3.1244061 0.0085896057 0.13938632 0.0018362816 0.0022783681 1.7693295 0 -3.048335 0.39646633 -3.0464988 0.64277703 -3.0466925 1 -3.0487771
|
||||
266 0.099868725 0.086180598 3.1401661 0.0070922949 0.095128081 0.001842608 0.002286044 1.7685191 0 -3.048334 0.41231024 -3.0464914 0.65425179 -3.0467252 1 -3.0487774
|
||||
9
examples/neb/log.19Jun17.neb.hop1.g++.4
Normal file
9
examples/neb/log.19Jun17.neb.hop1.g++.4
Normal file
@ -0,0 +1,9 @@
|
||||
LAMMPS (19 May 2017)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
|
||||
87 0.095951502 0.052720903 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
87 0.14137277 0.11108954 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
|
||||
124 0.099583263 0.085936899 0.0044220372 0.023873795 0.091308308 0.0071061754 0.0022863931 2.308121 0 -3.0535968 0.32223905 -3.0473329 0.61673898 -3.0464906 1 -3.048777
|
||||
9
examples/neb/log.19Jun17.neb.hop1.g++.8
Normal file
9
examples/neb/log.19Jun17.neb.hop1.g++.8
Normal file
@ -0,0 +1,9 @@
|
||||
LAMMPS (19 May 2017)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
|
||||
87 0.095951792 0.052720902 0.0055889267 0.065110091 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
87 0.14137297 0.11108954 0.0055889267 0.065110091 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775
|
||||
124 0.099582186 0.08593683 0.0044220345 0.023873731 0.091308197 0.0071061754 0.0022863931 2.3081211 0 -3.0535968 0.32223904 -3.0473329 0.61673896 -3.0464906 1 -3.048777
|
||||
12
examples/neb/log.19Jun17.neb.hop2.g++.4
Normal file
12
examples/neb/log.19Jun17.neb.hop2.g++.4
Normal file
@ -0,0 +1,12 @@
|
||||
LAMMPS (19 May 2017)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 14.104748 10.419633 0.1227071 4.999238 8.2087606 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
|
||||
100 0.24646695 0.10792196 0.0077146918 0.058733261 0.63504706 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
|
||||
200 0.061777741 0.050288749 0.0047486883 0.0095236035 0.88698597 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
|
||||
261 0.048699591 0.038138604 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
261 0.95753855 0.94297239 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
|
||||
361 0.072509627 0.06580631 0.0027545765 0.0044749366 0.016746483 0.0016018879 0.0016017805 1.1704611 0 -3.0514943 0.28176307 -3.0503855 0.50355454 -3.0498924 1 -3.0514942
|
||||
381 0.04884836 0.040787876 0.0023445904 0.0035162935 0.017959209 0.0016017716 0.0016016898 1.1713862 0 -3.0514943 0.27120138 -3.0504399 0.50428218 -3.0498925 1 -3.0514942
|
||||
12
examples/neb/log.19Jun17.neb.hop2.g++.8
Normal file
12
examples/neb/log.19Jun17.neb.hop2.g++.8
Normal file
@ -0,0 +1,12 @@
|
||||
LAMMPS (19 May 2017)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 14.104748 10.419633 0.1227071 4.999238 8.2087606 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
|
||||
100 0.24646695 0.10792196 0.0077146918 0.058733261 0.63504706 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
|
||||
200 0.061777741 0.050288749 0.0047486883 0.0095236035 0.88698597 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
|
||||
261 0.048699591 0.038138604 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
261 0.95753855 0.94297239 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494
|
||||
361 0.072509627 0.06580631 0.0027545765 0.0044749366 0.016746483 0.0016018879 0.0016017805 1.1704611 0 -3.0514943 0.28176307 -3.0503855 0.50355454 -3.0498924 1 -3.0514942
|
||||
381 0.04884836 0.040787876 0.0023445904 0.0035162935 0.017959209 0.0016017716 0.0016016898 1.1713862 0 -3.0514943 0.27120138 -3.0504399 0.50428218 -3.0498925 1 -3.0514942
|
||||
17
examples/neb/log.19Jun17.neb.sivac.g++.4
Normal file
17
examples/neb/log.19Jun17.neb.sivac.g++.4
Normal file
@ -0,0 +1,17 @@
|
||||
LAMMPS (19 May 2017)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
|
||||
10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253
|
||||
20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346
|
||||
30 0.094973707 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367
|
||||
40 0.027727472 0.0044528145 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337
|
||||
50 0.019429348 0.0030110281 0.0087135563 0.015391975 0.76952681 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372
|
||||
60 0.019009471 0.0016234562 0.0053426307 0.0086166186 0.77759617 0.38936861 0.38933364 1.7610433 0 -2213.3374 0.33187548 -2212.9523 0.66497617 -2212.948 1 -2213.3373
|
||||
63 0.0097365134 0.0012734598 0.004777604 0.0076121987 0.77865149 0.38888778 0.38886047 1.7615294 0 -2213.3374 0.33212107 -2212.952 0.66525385 -2212.9485 1 -2213.3373
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
63 0.77865149 0.31085821 0.004777604 0.0076121987 0.77865149 0.38888778 0.38886047 1.7615294 0 -2213.3374 0.33212107 -2212.952 0.66525385 -2212.9485 1 -2213.3373
|
||||
73 0.098175496 0.033609035 0.0027886955 0.0042742148 0.036594003 0.51024838 0.51023983 1.7607181 0 -2213.3374 0.27574151 -2213.0416 0.50432348 -2212.8271 1 -2213.3374
|
||||
83 0.03341862 0.012760857 0.0020868177 0.0031625649 0.010189924 0.51014634 0.51014168 1.7602562 0 -2213.3374 0.26045338 -2213.0672 0.50355193 -2212.8272 1 -2213.3374
|
||||
93 0.0097374358 0.0028416114 0.0014003718 0.0020986584 0.0053485291 0.51011052 0.51010848 1.7601202 0 -2213.3374 0.25397887 -2213.0783 0.50388111 -2212.8273 1 -2213.3374
|
||||
18
examples/neb/log.19Jun17.neb.sivac.g++.8
Normal file
18
examples/neb/log.19Jun17.neb.sivac.g++.8
Normal file
@ -0,0 +1,18 @@
|
||||
LAMMPS (19 May 2017)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959
|
||||
10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253
|
||||
20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346
|
||||
30 0.094973708 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367
|
||||
40 0.027727472 0.0044528144 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337
|
||||
50 0.019429341 0.0030110281 0.0087135565 0.015391975 0.7695268 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372
|
||||
60 0.019048963 0.0016262345 0.0053426844 0.0086167196 0.77759655 0.38936867 0.3893337 1.7610433 0 -2213.3374 0.33187545 -2212.9523 0.66497615 -2212.948 1 -2213.3373
|
||||
63 0.0097037048 0.0012761841 0.0047749367 0.0076075138 0.77865545 0.38888554 0.38885827 1.7615318 0 -2213.3374 0.33212221 -2212.952 0.66525512 -2212.9485 1 -2213.3373
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
63 0.77865545 0.3108551 0.0047749367 0.0076075138 0.77865545 0.38888554 0.38885827 1.7615318 0 -2213.3374 0.33212221 -2212.952 0.66525512 -2212.9485 1 -2213.3373
|
||||
73 0.098595989 0.033659485 0.0027927196 0.0042813387 0.038224344 0.51024759 0.51023901 1.7607156 0 -2213.3374 0.27595612 -2213.0413 0.50453988 -2212.8271 1 -2213.3374
|
||||
83 0.033344977 0.012868685 0.0020880608 0.0031645847 0.010250413 0.51014677 0.5101421 1.7602601 0 -2213.3374 0.26053624 -2213.067 0.50358775 -2212.8272 1 -2213.3374
|
||||
93 0.013254873 0.0038176141 0.0014928226 0.0022407967 0.0058577818 0.51011371 0.51011138 1.7601272 0 -2213.3374 0.25452741 -2213.0774 0.50382161 -2212.8273 1 -2213.3374
|
||||
95 0.0099964951 0.0031053214 0.0014131665 0.0021184362 0.0053683638 0.51011105 0.51010897 1.7601232 0 -2213.3374 0.2540975 -2213.0781 0.50387313 -2212.8273 1 -2213.3374
|
||||
@ -1,10 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 4327.2753 2746.3378 0.3387091 5.0075576 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
|
||||
100 0.10482184 0.085218486 0.014588241 0.066178594 0.19602237 0.0070900402 0.0022691875 2.3031875 0 -3.0535967 0.31839181 -3.0473647 0.63987598 -3.0465067 1 -3.0487759
|
||||
111 0.096708467 0.07803707 0.013922973 0.05417562 0.2023467 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
111 0.2023467 0.1777038 0.013922973 0.05417562 0.2023467 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764
|
||||
179 0.096874474 0.090676856 0.01040177 0.023364005 0.096874474 0.0071047642 0.0022856172 2.3122768 0 -3.0535969 0.31577311 -3.0473955 0.61798541 -3.0464922 1 -3.0487778
|
||||
@ -1,10 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 4327.2753 2746.3378 0.3387091 5.0075576 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
|
||||
100 0.10482171 0.085218406 0.014588234 0.066178435 0.19602242 0.0070900401 0.0022691875 2.3031875 0 -3.0535967 0.31839181 -3.0473647 0.639876 -3.0465067 1 -3.0487759
|
||||
111 0.096708718 0.078036984 0.013922966 0.054175505 0.20234693 0.0070871172 0.0022668002 2.3052946 0 -3.0535968 0.31853431 -3.0473633 0.64178873 -3.0465096 1 -3.0487764
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
111 0.20234693 0.17770387 0.013922966 0.054175505 0.20234693 0.0070871172 0.0022668002 2.3052946 0 -3.0535968 0.31853431 -3.0473633 0.64178873 -3.0465096 1 -3.0487764
|
||||
178 0.09975409 0.093814031 0.010577358 0.024247224 0.09975409 0.0071042931 0.0022851195 2.312004 0 -3.0535969 0.31607934 -3.0473923 0.618931 -3.0464926 1 -3.0487777
|
||||
@ -1,18 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
|
||||
100 0.24646695 0.10792196 0.01781018 0.098854684 0.63725646 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
|
||||
200 0.061777741 0.050288749 0.012466513 0.020420207 0.88741041 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
|
||||
300 0.056346766 0.030000618 0.0093152917 0.013765031 1.0101529 0.0014069751 0.0014068154 1.1699608 0 -3.0514942 0.30992449 -3.0502613 0.64174291 -3.0500873 1 -3.0514941
|
||||
400 0.025589489 0.015671005 0.0061287063 0.008588518 1.1136424 0.001370987 0.0013709154 1.1704204 0 -3.0514943 0.32016645 -3.0502198 0.65324019 -3.0501233 1 -3.0514943
|
||||
500 0.014778626 0.0092108366 0.0042668521 0.0059963914 1.1636579 0.0013527466 0.0013527072 1.1706283 0 -3.0514944 0.32550275 -3.0501993 0.65875414 -3.0501416 1 -3.0514943
|
||||
600 0.08786211 0.020876327 0.0031421548 0.0051657363 1.1898894 0.0013430848 0.0013430599 1.1707681 0 -3.0514944 0.32831927 -3.0501889 0.66160681 -3.0501513 1 -3.0514944
|
||||
633 0.0098132678 0.0055392541 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
633 1.1924486 1.1648685 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
|
||||
733 0.095331134 0.089136608 0.0021551441 0.0031844438 0.043042998 0.0016022317 0.0016022168 1.170789 0 -3.0514944 0.29157063 -3.0503375 0.50358402 -3.0498922 1 -3.0514944
|
||||
833 0.10539135 0.030724373 0.0013749699 0.002221013 0.10539135 0.0016019798 0.001601971 1.1732118 0 -3.0514944 0.26249002 -3.0504848 0.50415223 -3.0498924 1 -3.0514944
|
||||
933 0.01883894 0.011496399 0.0011058925 0.0018178041 0.014621806 0.0016018934 0.0016018865 1.173866 0 -3.0514944 0.25788763 -3.0505113 0.50466375 -3.0498925 1 -3.0514944
|
||||
996 0.0082457876 0.0036336551 0.00077325986 0.0013910671 0.0068823708 0.0016018293 0.0016018244 1.174511 0 -3.0514944 0.2544553 -3.0505324 0.50520462 -3.0498926 1 -3.0514944
|
||||
@ -1,18 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
|
||||
100 0.24646695 0.10792196 0.01781018 0.098854684 0.63725646 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
|
||||
200 0.061777741 0.050288749 0.012466513 0.020420207 0.88741041 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
|
||||
300 0.056346766 0.030000618 0.0093152917 0.013765031 1.0101529 0.0014069751 0.0014068154 1.1699608 0 -3.0514942 0.30992449 -3.0502613 0.64174291 -3.0500873 1 -3.0514941
|
||||
400 0.025589489 0.015671005 0.0061287063 0.008588518 1.1136424 0.001370987 0.0013709154 1.1704204 0 -3.0514943 0.32016645 -3.0502198 0.65324019 -3.0501233 1 -3.0514943
|
||||
500 0.014778626 0.0092108366 0.0042668521 0.0059963914 1.1636579 0.0013527466 0.0013527072 1.1706283 0 -3.0514944 0.32550275 -3.0501993 0.65875414 -3.0501416 1 -3.0514943
|
||||
600 0.08786211 0.020876327 0.0031421548 0.0051657363 1.1898894 0.0013430848 0.0013430599 1.1707681 0 -3.0514944 0.32831927 -3.0501889 0.66160681 -3.0501513 1 -3.0514944
|
||||
633 0.0098132678 0.0055392541 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
633 1.1924486 1.1648685 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
|
||||
733 0.095331134 0.089136608 0.0021551441 0.0031844438 0.043042998 0.0016022317 0.0016022168 1.170789 0 -3.0514944 0.29157063 -3.0503375 0.50358402 -3.0498922 1 -3.0514944
|
||||
833 0.10539135 0.030724373 0.0013749699 0.002221013 0.10539135 0.0016019798 0.001601971 1.1732118 0 -3.0514944 0.26249002 -3.0504848 0.50415223 -3.0498924 1 -3.0514944
|
||||
933 0.01883894 0.011496399 0.0011058925 0.0018178041 0.014621806 0.0016018934 0.0016018865 1.173866 0 -3.0514944 0.25788763 -3.0505113 0.50466375 -3.0498925 1 -3.0514944
|
||||
996 0.0082457876 0.0036336551 0.00077325986 0.0013910671 0.0068823708 0.0016018293 0.0016018244 1.174511 0 -3.0514944 0.2544553 -3.0505324 0.50520462 -3.0498926 1 -3.0514944
|
||||
@ -1,14 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
Running on 3 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
|
||||
10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
|
||||
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
|
||||
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
|
||||
40 0.0421393 0.0037035761 0.01173707 0.0421393 0.026104735 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
|
||||
50 0.025897844 0.0022804241 0.0081056535 0.025897844 0.016908913 0.5101712 0.51008591 1.739143 0 -2213.3373 0.49923344 -2212.8272 1 -2213.3373
|
||||
59 0.00962839 0.0012946076 0.005657505 0.009365729 0.012040803 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
59 0.012040803 0.0031505502 0.005657505 0.009365729 0.012040803 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
|
||||
63 0.009152118 0.0016692472 0.0049645771 0.0081967836 0.009152118 0.51013743 0.51010776 1.7409028 0 -2213.3374 0.50022239 -2212.8272 1 -2213.3373
|
||||
@ -1,14 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
Running on 3 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
|
||||
10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
|
||||
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
|
||||
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
|
||||
40 0.042139305 0.0037035764 0.01173707 0.042139305 0.026104735 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
|
||||
50 0.025899631 0.0022805513 0.0081057075 0.025899631 0.016908929 0.5101712 0.51008591 1.739143 0 -2213.3373 0.49923345 -2212.8272 1 -2213.3373
|
||||
59 0.0096285044 0.0012946258 0.0056576061 0.0093678253 0.012040919 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
59 0.012040919 0.0031505771 0.0056576061 0.0093678253 0.012040919 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373
|
||||
63 0.0091523813 0.0016692845 0.0049647607 0.0081998372 0.0091523813 0.51013743 0.51010775 1.7409028 0 -2213.3374 0.50022236 -2212.8272 1 -2213.3373
|
||||
@ -1,14 +0,0 @@
|
||||
LAMMPS (5 Oct 2016)
|
||||
Running on 3 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
|
||||
10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
|
||||
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
|
||||
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
|
||||
40 0.042139318 0.0037035773 0.011737071 0.042139318 0.026104737 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
|
||||
50 0.025904121 0.0022808707 0.0081058431 0.025904121 0.016908969 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923346 -2212.8272 1 -2213.3373
|
||||
59 0.0096287928 0.0012946716 0.005657861 0.0093731008 0.01204121 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955696 -2212.8272 1 -2213.3373
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
59 0.01204121 0.0031506449 0.005657861 0.0093731008 0.01204121 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955696 -2212.8272 1 -2213.3373
|
||||
63 0.0091530442 0.0016693787 0.0049652227 0.0082075097 0.0091530442 0.51013743 0.51010775 1.7409027 0 -2213.3374 0.50022228 -2212.8272 1 -2213.3373
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -48,7 +48,7 @@ FixReaxCSpeciesKokkos::FixReaxCSpeciesKokkos(LAMMPS *lmp, int narg, char **arg)
|
||||
{
|
||||
kokkosable = 1;
|
||||
atomKK = (AtomKokkos *) atom;
|
||||
|
||||
|
||||
// NOTE: Could improve performance if a Kokkos version of ComputeSpecAtom is added
|
||||
|
||||
datamask_read = X_MASK | V_MASK | Q_MASK | MASK_MASK;
|
||||
@ -116,35 +116,30 @@ void FixReaxCSpeciesKokkos::FindMolecule()
|
||||
done = 1;
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
if (!(mask[i] & groupbit)) continue;
|
||||
i = ilist[ii];
|
||||
if (!(mask[i] & groupbit)) continue;
|
||||
|
||||
itype = atom->type[i];
|
||||
itype = atom->type[i];
|
||||
|
||||
for (jj = 0; jj < MAXSPECBOND; jj++) {
|
||||
j = reaxc->tmpid[i][jj];
|
||||
j = reaxc->tmpid[i][jj];
|
||||
|
||||
if (j < i) continue;
|
||||
if (!(mask[j] & groupbit)) continue;
|
||||
if ((j == 0) && (j < i)) continue;
|
||||
if (!(mask[j] & groupbit)) continue;
|
||||
|
||||
if (clusterID[i] == clusterID[j] && PBCconnected[i] == PBCconnected[j]
|
||||
&& x0[i].x == x0[j].x && x0[i].y == x0[j].y && x0[i].z == x0[j].z) continue;
|
||||
if (clusterID[i] == clusterID[j]
|
||||
&& x0[i].x == x0[j].x && x0[i].y == x0[j].y && x0[i].z == x0[j].z) continue;
|
||||
|
||||
jtype = atom->type[j];
|
||||
bo_cut = BOCut[itype][jtype];
|
||||
bo_tmp = spec_atom[i][jj+7];
|
||||
bo_cut = BOCut[itype][jtype];
|
||||
bo_tmp = spec_atom[i][jj+7];
|
||||
|
||||
if (bo_tmp > bo_cut) {
|
||||
if (bo_tmp > bo_cut) {
|
||||
clusterID[i] = clusterID[j] = MIN(clusterID[i], clusterID[j]);
|
||||
PBCconnected[i] = PBCconnected[j] = MAX(PBCconnected[i], PBCconnected[j]);
|
||||
x0[i] = x0[j] = chAnchor(x0[i], x0[j]);
|
||||
if ((fabs(spec_atom[i][1] - spec_atom[j][1]) > reaxc->control->bond_cut)
|
||||
|| (fabs(spec_atom[i][2] - spec_atom[j][2]) > reaxc->control->bond_cut)
|
||||
|| (fabs(spec_atom[i][3] - spec_atom[j][3]) > reaxc->control->bond_cut))
|
||||
PBCconnected[i] = PBCconnected[j] = 1;
|
||||
done = 0;
|
||||
}
|
||||
}
|
||||
done = 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
if (!done) change = 1;
|
||||
if (done) break;
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -25,6 +25,7 @@
|
||||
#include <string.h>
|
||||
#include "pair_lj_charmmfsw_coul_long.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "kspace.h"
|
||||
@ -61,6 +62,15 @@ PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(LAMMPS *lmp) : Pair(lmp)
|
||||
// short-range/long-range flag accessed by DihedralCharmmfsw
|
||||
|
||||
dihedflag = 1;
|
||||
|
||||
// switch qqr2e from LAMMPS value to CHARMM value
|
||||
|
||||
if (strcmp(update->unit_style,"real") == 0) {
|
||||
if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real))
|
||||
error->message(FLERR,"Switching to CHARMM coulomb energy"
|
||||
" conversion constant");
|
||||
force->qqr2e = force->qqr2e_charmm_real;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -87,6 +97,15 @@ PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong()
|
||||
}
|
||||
if (ftable) free_tables();
|
||||
}
|
||||
|
||||
// switch qqr2e back from CHARMM value to LAMMPS value
|
||||
|
||||
if (update && strcmp(update->unit_style,"real") == 0) {
|
||||
if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real))
|
||||
error->message(FLERR,"Restoring original LAMMPS coulomb energy"
|
||||
" conversion constant");
|
||||
force->qqr2e = force->qqr2e_lammps_real;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -1337,8 +1337,8 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
|
||||
fH[1] = 0.5 * alpha * fd[1];
|
||||
fH[2] = 0.5 * alpha * fd[2];
|
||||
|
||||
xH1 = x[jH1];
|
||||
xH2 = x[jH2];
|
||||
xH1 = x[iH1];
|
||||
xH2 = x[iH2];
|
||||
v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
|
||||
v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
|
||||
v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
|
||||
|
||||
@ -8,7 +8,7 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpiicpc
|
||||
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
|
||||
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
|
||||
CCFLAGS = -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \
|
||||
-fno-alias -ansi-alias -restrict $(OPTFLAGS)
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
@ -8,7 +8,7 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpiicpc
|
||||
MIC_OPT = -qoffload-arch=mic-avx512 -fp-model fast=2
|
||||
CCFLAGS = -g -O3 -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \
|
||||
CCFLAGS = -O3 -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64 \
|
||||
-xHost -fno-alias -ansi-alias -restrict \
|
||||
-qoverride-limits $(MIC_OPT)
|
||||
SHFLAGS = -fPIC
|
||||
|
||||
@ -8,7 +8,7 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpiicpc
|
||||
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
|
||||
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
|
||||
CCFLAGS = -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \
|
||||
-fno-alias -ansi-alias -restrict $(OPTFLAGS)
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
@ -1271,7 +1271,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
|
||||
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
|
||||
double cross321[3],cross234[3],prefactor,SpN;
|
||||
double fcijpc,fcikpc,fcjlpc,fcjkpc,fcilpc;
|
||||
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
|
||||
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa2,at2,cw,cwnum,cwnom;
|
||||
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
|
||||
double dctik,dctjk,dctjl,dctij,dctji,dctil,rik2i,rjl2i,sink2i,sinl2i;
|
||||
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil,dt1dij;
|
||||
@ -1856,8 +1856,6 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
|
||||
|
||||
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa1 = -prefactor*(1.0-square(om1234)) *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
|
||||
at2 = aa*cwnum;
|
||||
|
||||
@ -2107,7 +2105,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
|
||||
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
|
||||
double cross321[3],cross234[3],prefactor,SpN;
|
||||
double fcikpc,fcjlpc,fcjkpc,fcilpc;
|
||||
double dt2dik[3],dt2djl[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
|
||||
double dt2dik[3],dt2djl[3],aa,aaa2,at2,cw,cwnum,cwnom;
|
||||
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
|
||||
double dctik,dctjk,dctjl,dctil,rik2i,rjl2i,sink2i,sinl2i;
|
||||
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil;
|
||||
@ -2800,8 +2798,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
|
||||
|
||||
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa1 = -prefactor*(1.0-square(om1234)) *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
|
||||
at2 = aa*cwnum;
|
||||
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
@ -18,6 +18,7 @@
|
||||
#include <mpi.h>
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "dihedral_charmm.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
@ -26,6 +27,7 @@
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "update.h"
|
||||
#include "respa.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
@ -368,10 +370,26 @@ void DihedralCharmm::coeff(int narg, char **arg)
|
||||
|
||||
void DihedralCharmm::init_style()
|
||||
{
|
||||
if (strstr(update->integrate_style,"respa")) {
|
||||
Respa *r = (Respa *) update->integrate;
|
||||
if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
|
||||
error->all(FLERR,"Dihedral style charmm must be set to same"
|
||||
" r-RESPA level as 'pair'");
|
||||
if (r->level_outer >= 0 && (r->level_outer != r->level_dihedral))
|
||||
error->all(FLERR,"Dihedral style charmm must be set to same"
|
||||
" r-RESPA level as 'outer'");
|
||||
}
|
||||
|
||||
// insure use of CHARMM pair_style if any weight factors are non-zero
|
||||
// set local ptrs to LJ 14 arrays setup by Pair
|
||||
// also verify that the correct 1-4 scaling is set
|
||||
|
||||
if (weightflag) {
|
||||
|
||||
if ((force->special_lj[3] != 0.0) || (force->special_coul[3] != 0.0))
|
||||
error->all(FLERR,"Must use 'special_bonds charmm' with"
|
||||
" dihedral style charmm for use with CHARMM pair styles");
|
||||
|
||||
int itmp;
|
||||
if (force->pair == NULL)
|
||||
error->all(FLERR,"Dihedral charmm is incompatible with Pair style");
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user