forked from lijiext/lammps
Merge branch 'master' into kim-simulator-models
This commit is contained in:
Ryan S. Elliott
commit
03d26f6f6f
|
|
@ -37,7 +37,7 @@ include(PreventInSourceBuilds)
|
|||
|
||||
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
|
||||
#release comes with -O3 by default
|
||||
set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
|
||||
set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
|
||||
endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
|
||||
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
|
||||
|
||||
|
|
@ -673,5 +673,10 @@ if(PKG_KOKKOS)
|
|||
message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
|
||||
endif()
|
||||
if(PKG_KSPACE)
|
||||
message(STATUS "Using ${FFT} as FFT")
|
||||
message(STATUS "Using ${FFT} as primary FFT library")
|
||||
if(FFT_SINGLE)
|
||||
message(STATUS "Using single precision FFTs")
|
||||
else()
|
||||
message(STATUS "Using double precision FFTs")
|
||||
endif()
|
||||
endif()
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
if(PKG_KSPACE)
|
||||
option(FFT_SINGLE "Use single precision FFT instead of double" OFF)
|
||||
option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
|
||||
set(FFTW "FFTW3")
|
||||
if(FFT_SINGLE)
|
||||
set(FFTW "FFTW3F")
|
||||
|
|
@ -7,26 +7,30 @@ if(PKG_KSPACE)
|
|||
endif()
|
||||
find_package(${FFTW} QUIET)
|
||||
if(${FFTW}_FOUND)
|
||||
set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
|
||||
set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
|
||||
else()
|
||||
set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
|
||||
endif()
|
||||
set(FFT_VALUES KISS ${FFTW} MKL)
|
||||
set(FFT_VALUES KISS FFTW3 MKL)
|
||||
set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
|
||||
validate_option(FFT FFT_VALUES)
|
||||
string(TOUPPER ${FFT} FFT)
|
||||
if(NOT FFT STREQUAL "KISS")
|
||||
find_package(${FFT} REQUIRED)
|
||||
if(NOT FFT STREQUAL "FFTW3F")
|
||||
add_definitions(-DFFT_FFTW)
|
||||
else()
|
||||
add_definitions(-DFFT_${FFT})
|
||||
endif()
|
||||
include_directories(${${FFT}_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
|
||||
|
||||
if(FFT STREQUAL "FFTW3")
|
||||
find_package(${FFTW} REQUIRED)
|
||||
add_definitions(-DFFT_FFTW3)
|
||||
include_directories(${${FFTW}_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
|
||||
elseif(FFT STREQUAL "MKL")
|
||||
find_package(MKL REQUIRED)
|
||||
add_definitions(-DFFT_MKL)
|
||||
include_directories(${MKL_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
|
||||
else()
|
||||
# last option is KISSFFT
|
||||
add_definitions(-DFFT_KISS)
|
||||
endif()
|
||||
|
||||
set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
|
||||
set(FFT_PACK_VALUES array pointer memcpy)
|
||||
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
.TH LAMMPS "18 June 2019" "2019-06-18"
|
||||
.TH LAMMPS "19 July 2019" "2019-07-19"
|
||||
.SH NAME
|
||||
.B LAMMPS
|
||||
\- Molecular Dynamics Simulator.
|
||||
|
|
|
|||
|
|
@ -5900,6 +5900,11 @@ The element names in the ADP file do not match those requested. :dd
|
|||
|
||||
The element names in the EAM file do not match those requested. :dd
|
||||
|
||||
{Incorrect format of ... section in data file} :dt
|
||||
|
||||
Number or type of values per line in the given section of the data file
|
||||
is not consistent with the requirements for this section. :dd
|
||||
|
||||
{Incorrect format in COMB potential file} :dt
|
||||
|
||||
Incorrect number of words per line in the potential file. :dd
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="18 Jun 2019 version">
|
||||
<META NAME="docnumber" CONTENT="19 Jul 2019 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 @@
|
|||
:line
|
||||
|
||||
LAMMPS Documentation :c,h1
|
||||
18 Jun 2019 version :c,h2
|
||||
19 Jul 2019 version :c,h2
|
||||
|
||||
"What is a LAMMPS version?"_Manual_version.html
|
||||
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -171,42 +171,40 @@ The individual style names on the "Commands
|
|||
compute"_Commands_compute.html doc page are followed by one or more of
|
||||
(g,i,k,o,t) to indicate which accelerated styles exist.
|
||||
|
||||
"ackland/atom"_compute_ackland_atom.html -
|
||||
"ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation
|
||||
"adf"_compute_adf.html - angular distribution function of triples of atoms
|
||||
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
|
||||
"angle"_compute_angle.html -
|
||||
"angle/local"_compute_angle_local.html -
|
||||
"angle/local"_compute_bond_local.html - theta and energy of each angle
|
||||
"angle"_compute_angle.html - energy of each angle sub-style
|
||||
"angle/local"_compute_angle_local.html - theta and energy of each angle
|
||||
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
|
||||
"basal/atom"_compute_basal_atom.html -
|
||||
"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom
|
||||
"body/local"_compute_body_local.html - attributes of body sub-particles
|
||||
"bond"_compute_bond.html - values computed by a bond style
|
||||
"bond"_compute_bond.html - energy of each bond sub-style
|
||||
"bond/local"_compute_bond_local.html - distance and energy of each bond
|
||||
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
|
||||
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
|
||||
"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
|
||||
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
|
||||
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
|
||||
"cnp/atom"_compute_cnp_atom.html -
|
||||
"cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom
|
||||
"com"_compute_com.html - center-of-mass of group of atoms
|
||||
"com/chunk"_compute_com_chunk.html - center-of-mass for each chunk
|
||||
"contact/atom"_compute_contact_atom.html - contact count for each spherical particle
|
||||
"coord/atom"_compute_coord_atom.html - coordination number for each atom
|
||||
"damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
|
||||
"dihedral"_compute_dihedral.html -
|
||||
"dihedral"_compute_dihedral.html - energy of each dihedral sub-style
|
||||
"dihedral/local"_compute_dihedral_local.html - angle of each dihedral
|
||||
"dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom
|
||||
"dipole/chunk"_compute_dipole_chunk.html -
|
||||
"dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk
|
||||
"displace/atom"_compute_displace_atom.html - displacement of each atom
|
||||
"dpd"_compute_dpd.html -
|
||||
"dpd/atom"_compute_dpd_atom.html -
|
||||
"edpd/temp/atom"_compute_edpd_temp_atom.html -
|
||||
"entropy/atom"_compute_entropy_atom.html -
|
||||
"edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group
|
||||
"entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom
|
||||
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
|
||||
"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
|
||||
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
|
||||
"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
|
||||
"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
|
||||
"erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle
|
||||
"event/displace"_compute_event_displace.html - detect event on atom displacement
|
||||
"fep"_compute_fep.html -
|
||||
"force/tally"_compute_tally.html -
|
||||
|
|
@ -218,17 +216,17 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
|||
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
|
||||
"heat/flux/tally"_compute_tally.html -
|
||||
"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
|
||||
"improper"_compute_improper.html -
|
||||
"improper"_compute_improper.html - energy of each improper sub-style
|
||||
"improper/local"_compute_improper_local.html - angle of each improper
|
||||
"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
|
||||
"ke"_compute_ke.html - translational kinetic energy
|
||||
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
|
||||
"ke/atom/eff"_compute_ke_atom_eff.html -
|
||||
"ke/eff"_compute_ke_eff.html -
|
||||
"ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model
|
||||
"ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model
|
||||
"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
|
||||
"meso/e/atom"_compute_meso_e_atom.html -
|
||||
"meso/rho/atom"_compute_meso_rho_atom.html -
|
||||
"meso/t/atom"_compute_meso_t_atom.html -
|
||||
"meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
|
||||
"meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
|
||||
"meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
|
||||
"msd"_compute_msd.html - mean-squared displacement of group of atoms
|
||||
"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
|
||||
"msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
|
||||
|
|
@ -242,73 +240,72 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
|||
"pe/tally"_compute_tally.html -
|
||||
"plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
|
||||
"pressure"_compute_pressure.html - total pressure and pressure tensor
|
||||
"pressure/cylinder"_compute_pressure_cylinder.html -
|
||||
"pressure/uef"_compute_pressure_uef.html -
|
||||
"pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates
|
||||
"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field
|
||||
"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
|
||||
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
|
||||
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
|
||||
"ptm/atom"_compute_ptm_atom.html -
|
||||
"ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method
|
||||
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
|
||||
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
|
||||
"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
|
||||
"reduce/region"_compute_reduce.html - same as compute reduce, within a region
|
||||
"rigid/local"_compute_rigid_local.html - extract rigid body attributes
|
||||
"saed"_compute_saed.html -
|
||||
"saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes
|
||||
"slice"_compute_slice.html - extract values from global vector or array
|
||||
"smd/contact/radius"_compute_smd_contact_radius.html -
|
||||
"smd/damage"_compute_smd_damage.html -
|
||||
"smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics
|
||||
"smd/hourglass/error"_compute_smd_hourglass_error.html -
|
||||
"smd/internal/energy"_compute_smd_internal_energy.html -
|
||||
"smd/plastic/strain"_compute_smd_plastic_strain.html -
|
||||
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
|
||||
"smd/rho"_compute_smd_rho.html -
|
||||
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
|
||||
"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
|
||||
"smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics
|
||||
"smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics
|
||||
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics
|
||||
"smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics
|
||||
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics
|
||||
"smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics
|
||||
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
|
||||
"smd/tlsph/shape"_compute_smd_tlsph_shape.html -
|
||||
"smd/tlsph/strain"_compute_smd_tlsph_strain.html -
|
||||
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
|
||||
"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
|
||||
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
|
||||
"smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles
|
||||
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
|
||||
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
|
||||
"smd/ulsph/strain"_compute_smd_ulsph_strain.html -
|
||||
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
|
||||
"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
|
||||
"smd/vol"_compute_smd_vol.html -
|
||||
"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
|
||||
"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
|
||||
"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
|
||||
"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
|
||||
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
|
||||
"spin"_compute_spin.html -
|
||||
"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
|
||||
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
|
||||
"stress/mop"_compute_stress_mop.html -
|
||||
"stress/mop/profile"_compute_stress_mop.html -
|
||||
"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
|
||||
"stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes
|
||||
"stress/tally"_compute_tally.html -
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle
|
||||
"temp"_compute_temp.html - temperature of group of atoms
|
||||
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
|
||||
"temp/body"_compute_temp_body.html - temperature of body particles
|
||||
"temp/chunk"_compute_temp_chunk.html - temperature of each chunk
|
||||
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
|
||||
"temp/cs"_compute_temp_cs.html -
|
||||
"temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other
|
||||
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
|
||||
"temp/deform/eff"_compute_temp_deform_eff.html -
|
||||
"temp/drude"_compute_temp_drude.html -
|
||||
"temp/eff"_compute_temp_eff.html -
|
||||
"temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model
|
||||
"temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs
|
||||
"temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model
|
||||
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
|
||||
"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
|
||||
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
|
||||
"temp/region"_compute_temp_region.html - temperature of a region of atoms
|
||||
"temp/region/eff"_compute_temp_region_eff.html -
|
||||
"temp/rotate"_compute_temp_rotate.html -
|
||||
"temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model
|
||||
"temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities
|
||||
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
|
||||
"temp/uef"_compute_temp_uef.html -
|
||||
"temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field
|
||||
"ti"_compute_ti.html - thermodynamic integration free energy values
|
||||
"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
|
||||
"vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms
|
||||
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
|
||||
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom
|
||||
"xrd"_compute_xrd.html - :ul
|
||||
"xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -57,8 +57,7 @@ Boolean expression is FALSE, then no commands are executed.
|
|||
The syntax for Boolean expressions is described below.
|
||||
|
||||
Each command (t1, f1, e1, etc) can be any valid LAMMPS input script
|
||||
command, except an "include"_include.html command, which is not
|
||||
allowed. If the command is more than one word, it must enclosed in
|
||||
command. If the command is more than one word, it must enclosed in
|
||||
quotes, so it will be treated as a single argument, as in the examples
|
||||
above.
|
||||
|
||||
|
|
|
|||
|
|
@ -147,7 +147,8 @@ asub = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre
|
|||
|
||||
The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
|
||||
standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b
|
||||
parameters are the standard beta parameters). The rozero parameter is
|
||||
parameters are the standard beta parameters). Note that only parameters
|
||||
normalized to t0 = 1.0 are supported. The rozero parameter is
|
||||
an element-dependent density scaling that weights the reference
|
||||
background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and
|
||||
is typically 1.0 for single-element systems. The ibar parameter
|
||||
|
|
|
|||
|
|
@ -23,9 +23,11 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs
|
|||
style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
|
||||
args = list of arguments for these particular styles :ul
|
||||
|
||||
{oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
{oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
xi = temperature-independent coefficient in stacking strength
|
||||
kappa = coefficient of linear temperature dependence in stacking strength
|
||||
{oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
|
||||
|
|
@ -34,7 +36,7 @@ args = list of arguments for these particular styles :ul
|
|||
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
|
@ -62,7 +64,7 @@ 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). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)
|
||||
Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
|
||||
and the first coefficient after {oxdna/hbond} (seq=seqdep 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
|
||||
|
|
|
|||
|
|
@ -24,10 +24,12 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/
|
|||
style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
|
||||
args = list of arguments for these particular styles :ul
|
||||
|
||||
{oxdna2/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
{oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
|
||||
T = temperature (oxDNA units, 0.1 = 300 K)
|
||||
{oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
xi = temperature-independent coefficient in stacking strength
|
||||
kappa = coefficient of linear temperature dependence in stacking strength
|
||||
{oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
|
||||
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
|
||||
{oxdna2/dh} args = T rhos qeff
|
||||
|
|
@ -39,7 +41,7 @@ args = list of arguments for these particular styles :ul
|
|||
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
|
@ -68,8 +70,8 @@ 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). Most of the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
|
||||
Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
|
||||
the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients
|
||||
Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
|
||||
the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three 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.
|
||||
|
|
|
|||
|
|
@ -565,6 +565,7 @@ molecular: atom-ID molecule-ID atom-type x y z
|
|||
peri: atom-ID atom-type volume density x y z
|
||||
smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z
|
||||
sphere: atom-ID atom-type diameter density x y z
|
||||
spin: atom-ID atom-type sp x y z spx spy spz
|
||||
template: atom-ID molecule-ID template-index template-atom atom-type x y z
|
||||
tri: atom-ID molecule-ID atom-type triangleflag density x y z
|
||||
wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
|
||||
|
|
@ -595,6 +596,8 @@ mux,muy,muz = components of dipole moment of atom (dipole units)
|
|||
q = charge on atom (charge units)
|
||||
rho = density (need units) for SPH particles
|
||||
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
|
||||
sp = norm of magnetic spin of atom (in number of Bohr magnetons)
|
||||
spx,spy,spz = components of magnetic spin of atom (adim normalized vector)
|
||||
template-atom = which atom within a template molecule the atom is
|
||||
template-index = which molecule within the molecule template the atom is part of
|
||||
theta = internal temperature of a DPD particle
|
||||
|
|
|
|||
|
|
@ -1525,6 +1525,7 @@ Magdeburg
|
|||
magelec
|
||||
Maginn
|
||||
magneton
|
||||
magnetons
|
||||
mainboard
|
||||
mainboards
|
||||
makefile
|
||||
|
|
|
|||
|
|
@ -22,6 +22,17 @@ A - C - G - T - A - C - G - T
|
|||
| | | | | | | |
|
||||
T - G - C - A T - G - C - A
|
||||
|
||||
/examples/duplex3:
|
||||
This is basically the duplex1 run with sequence-dependent stacking
|
||||
and hydrogen-bonding strengths enabled and both nucleotide mass and
|
||||
moment of inertia set to the value of the standalone implementation
|
||||
of oxDNA (M = I = 1). To achieve this, the masses can be set directly
|
||||
in the input and data file, whereas the moment of inertia is set via
|
||||
the diameter of the ellipsoid in the data file and has a value of 3.16227766.
|
||||
The change of mass and moment of inertia allows direct comparision of
|
||||
e.g. trajectory data, energies or time-dependent observables on a per-timestep
|
||||
basis until numerical noise causes deviations at later simulation times.
|
||||
|
||||
/util:
|
||||
This directory contains a simple python setup tool which creates
|
||||
single straight or helical DNA strands, DNA duplexes or arrays of DNA
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ Atoms
|
|||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
|
|
@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
|
@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
|
|||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
|
|
@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -1,172 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
|
||||
1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
|
||||
2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
|
||||
3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
|
||||
4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
|
||||
5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
|
||||
6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
|
||||
7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
|
||||
8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
|
||||
9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
|
||||
10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
|
||||
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05
|
||||
Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 60875.649 tau/day, 70457.927 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79
|
||||
Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96
|
||||
Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00
|
||||
Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61
|
||||
Other | | 0.002982 | | | 2.10
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 43 ave 43 max 43 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 43
|
||||
Ave neighs/atom = 4.3
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,172 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
|
||||
1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
|
||||
2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
|
||||
3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892
|
||||
4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436
|
||||
5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104
|
||||
6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875
|
||||
7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172
|
||||
8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611
|
||||
9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514
|
||||
10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398
|
||||
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899
|
||||
Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 64220.659 tau/day, 74329.466 timesteps/s
|
||||
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81
|
||||
Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47
|
||||
Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04
|
||||
Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42
|
||||
Other | | 0.05989 | | | 44.52
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 17.5 ave 33 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 70
|
||||
Ave neighs/atom = 7
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -38,7 +38,7 @@ Atoms
|
|||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
|
|
@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
|
@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
|
|||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
|
|
@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -1,172 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||
1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
|
||||
2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
|
||||
3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
|
||||
4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832
|
||||
5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266
|
||||
6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964
|
||||
7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
|
||||
8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989
|
||||
9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
|
||||
10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
|
||||
10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809
|
||||
Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 29234.801 tau/day, 33836.575 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 | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92
|
||||
Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56
|
||||
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||
Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74
|
||||
Other | | 0.003813 | | | 1.29
|
||||
|
||||
Nlocal: 16 ave 16 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 88 ave 88 max 88 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 88
|
||||
Ave neighs/atom = 5.5
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,172 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||
1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
|
||||
2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504
|
||||
3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198
|
||||
4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506
|
||||
5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
|
||||
6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
|
||||
7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
|
||||
8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614
|
||||
9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
|
||||
10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463
|
||||
10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05
|
||||
Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 34303.820 tau/day, 39703.495 timesteps/s
|
||||
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55
|
||||
Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94
|
||||
Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02
|
||||
Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27
|
||||
Other | | 0.1208 | | | 47.96
|
||||
|
||||
Nlocal: 4 ave 8 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 9 ave 10 max 8 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 34.5 ave 67 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 138
|
||||
Ave neighs/atom = 8.625
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -32,7 +32,7 @@ Atoms
|
|||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
|
|
@ -30,19 +31,19 @@ bond_coeff * 2.0 0.25 0.7564
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
|
|
@ -73,6 +74,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -1,178 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||
3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||
4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||
5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||
6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157
|
||||
7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036
|
||||
8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962
|
||||
9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899
|
||||
10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815
|
||||
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||
Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 57828.835 tau/day, 66931.522 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12
|
||||
Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91
|
||||
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||
Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68
|
||||
Other | | 0.004268 | | | 2.86
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 45 ave 45 max 45 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 45
|
||||
Ave neighs/atom = 4.5
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,178 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||
3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||
4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||
5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||
6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156
|
||||
7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036
|
||||
8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962
|
||||
9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899
|
||||
10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815
|
||||
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||
Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 59247.054 tau/day, 68572.979 timesteps/s
|
||||
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12
|
||||
Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24
|
||||
Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04
|
||||
Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38
|
||||
Other | | 0.06674 | | | 45.76
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 18.5 ave 35 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 74
|
||||
Ave neighs/atom = 7.4
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -38,7 +38,7 @@ Atoms
|
|||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
variable T equal 0.1
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
|
@ -30,19 +30,19 @@ bond_coeff * 2.0 0.25 0.7564
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
|
|
@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -1,178 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
|
||||
2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591
|
||||
3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324
|
||||
4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247
|
||||
5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361
|
||||
6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178
|
||||
7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928
|
||||
8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092
|
||||
9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833
|
||||
10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566
|
||||
10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454
|
||||
Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 26356.746 tau/day, 30505.493 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86
|
||||
Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44
|
||||
Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00
|
||||
Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37
|
||||
Other | | 0.003398 | | | 1.04
|
||||
|
||||
Nlocal: 16 ave 16 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 116 ave 116 max 116 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 116
|
||||
Ave neighs/atom = 7.25
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,178 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
|
||||
2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481
|
||||
3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125
|
||||
4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703
|
||||
5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963
|
||||
6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531
|
||||
7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691
|
||||
8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058
|
||||
9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658
|
||||
10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535
|
||||
10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05
|
||||
Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 29625.313 tau/day, 34288.557 timesteps/s
|
||||
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96
|
||||
Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19
|
||||
Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02
|
||||
Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17
|
||||
Other | | 0.139 | | | 47.65
|
||||
|
||||
Nlocal: 4 ave 8 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 11 ave 14 max 8 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 46 ave 89 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 184
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,73 @@
|
|||
# LAMMPS data file
|
||||
10 atoms
|
||||
10 ellipsoids
|
||||
8 bonds
|
||||
|
||||
4 atom types
|
||||
1 bond types
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
2 1.0
|
||||
3 1.0
|
||||
4 1.0
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
|
||||
7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
|
||||
8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
|
||||
7 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
|
||||
8 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
9 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
|
||||
10 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
|
@ -0,0 +1,79 @@
|
|||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex3
|
||||
|
||||
set atom * mass 1.0
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -15,7 +15,7 @@
|
|||
|
||||
#include "lal_answer.h"
|
||||
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define AnswerT Answer<numtyp,acctyp>
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
|
|
@ -311,4 +311,4 @@ void AnswerT::cq(const int cq_index) {
|
|||
}
|
||||
|
||||
template class Answer<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
|
||||
#include "lal_atom.h"
|
||||
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define AtomT Atom<numtyp,acctyp>
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
|
|
@ -349,4 +349,4 @@ void AtomT::compile_kernels(UCL_Device &dev) {
|
|||
#endif
|
||||
|
||||
template class Atom<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -14,7 +14,8 @@
|
|||
***************************************************************************/
|
||||
|
||||
#include "lal_base_atomic.h"
|
||||
using namespace LAMMPS_AL;
|
||||
|
||||
namespace LAMMPS_AL {
|
||||
#define BaseAtomicT BaseAtomic<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> global_device;
|
||||
|
|
@ -285,4 +286,4 @@ void BaseAtomicT::compile_kernels(UCL_Device &dev, const void *pair_str,
|
|||
}
|
||||
|
||||
template class BaseAtomic<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
***************************************************************************/
|
||||
|
||||
#include "lal_base_charge.h"
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BaseChargeT BaseCharge<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> global_device;
|
||||
|
|
@ -302,4 +302,4 @@ void BaseChargeT::compile_kernels(UCL_Device &dev, const void *pair_str,
|
|||
}
|
||||
|
||||
template class BaseCharge<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
***************************************************************************/
|
||||
|
||||
#include "lal_base_dipole.h"
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BaseDipoleT BaseDipole<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> global_device;
|
||||
|
|
@ -311,4 +311,4 @@ void BaseDipoleT::compile_kernels(UCL_Device &dev, const void *pair_str,
|
|||
}
|
||||
|
||||
template class BaseDipole<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
***************************************************************************/
|
||||
|
||||
#include "lal_base_dpd.h"
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BaseDPDT BaseDPD<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> global_device;
|
||||
|
|
@ -308,4 +308,4 @@ void BaseDPDT::compile_kernels(UCL_Device &dev, const void *pair_str,
|
|||
}
|
||||
|
||||
template class BaseDPD<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
|
||||
#include "lal_base_ellipsoid.h"
|
||||
#include <cstdlib>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
#if defined(USE_OPENCL)
|
||||
#include "ellipsoid_nbor_cl.h"
|
||||
|
|
@ -488,4 +488,4 @@ void BaseEllipsoidT::compile_kernels(UCL_Device &dev,
|
|||
}
|
||||
|
||||
template class BaseEllipsoid<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -14,7 +14,7 @@
|
|||
***************************************************************************/
|
||||
|
||||
#include "lal_base_three.h"
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BaseThreeT BaseThree<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> global_device;
|
||||
|
|
@ -397,4 +397,4 @@ void BaseThreeT::compile_kernels(UCL_Device &dev, const void *pair_str,
|
|||
}
|
||||
|
||||
template class BaseThree<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *beck=0;
|
|||
|
||||
#include "lal_beck.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BeckT Beck<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -150,3 +150,4 @@ void BeckT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Beck<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *born=0;
|
|||
|
||||
#include "lal_born.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BornT Born<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -179,3 +179,4 @@ void BornT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Born<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *born_coul_long=0;
|
|||
|
||||
#include "lal_born_coul_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BornCoulLongT BornCoulLong<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -173,3 +173,4 @@ void BornCoulLongT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class BornCoulLong<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *born_coul_long_cs=0;
|
|||
|
||||
#include "lal_born_coul_long_cs.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BornCoulLongCST BornCoulLongCS<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -93,3 +93,4 @@ int BornCoulLongCST::init(const int ntypes, double **host_cutsq, double **host_r
|
|||
}
|
||||
|
||||
template class BornCoulLongCS<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *born_coul_wolf=0;
|
|||
|
||||
#include "lal_born_coul_wolf.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BornCoulWolfT BornCoulWolf<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -174,3 +174,4 @@ void BornCoulWolfT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class BornCoulWolf<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *born_coul_wolf_cs=0;
|
|||
|
||||
#include "lal_born_coul_wolf_cs.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BornCoulWolfCST BornCoulWolfCS<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -95,3 +95,4 @@ int BornCoulWolfCST::init(const int ntypes, double **host_cutsq, double **host_r
|
|||
}
|
||||
|
||||
template class BornCoulWolfCS<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *buck=0;
|
|||
|
||||
#include "lal_buck.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BuckT Buck<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -168,3 +168,4 @@ void BuckT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Buck<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *buck_coul=0;
|
|||
|
||||
#include "lal_buck_coul.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BuckCoulT BuckCoul<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -161,3 +161,4 @@ void BuckCoulT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class BuckCoul<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *buck_coul_long=0;
|
|||
|
||||
#include "lal_buck_coul_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define BuckCoulLongT BuckCoulLong<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -166,3 +166,4 @@ void BuckCoulLongT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class BuckCoulLong<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *charmm_long=0;
|
|||
|
||||
#include "lal_charmm_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define CHARMMLongT CHARMMLong<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -174,3 +174,4 @@ void CHARMMLongT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class CHARMMLong<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *colloid=0;
|
|||
|
||||
#include "lal_colloid.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define ColloidT Colloid<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -179,3 +179,4 @@ void ColloidT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Colloid<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *coul=0;
|
|||
|
||||
#include "lal_coul.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define CoulT Coul<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -164,3 +164,4 @@ void CoulT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Coul<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *coul_debye=0;
|
|||
|
||||
#include "lal_coul_debye.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define CoulDebyeT CoulDebye<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -165,3 +165,4 @@ void CoulDebyeT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class CoulDebye<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *coul_dsf=0;
|
|||
|
||||
#include "lal_coul_dsf.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define CoulDSFT CoulDSF<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -151,3 +151,4 @@ void CoulDSFT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class CoulDSF<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *coul_long=0;
|
|||
|
||||
#include "lal_coul_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define CoulLongT CoulLong<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> pair_gpu_device;
|
||||
|
|
@ -156,3 +156,4 @@ void CoulLongT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class CoulLong<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *coul_long_cs=0;
|
|||
|
||||
#include "lal_coul_long_cs.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define CoulLongCST CoulLongCS<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> pair_gpu_device;
|
||||
|
|
@ -76,3 +76,4 @@ int CoulLongCST::init(const int ntypes, double **host_scale,
|
|||
}
|
||||
|
||||
template class CoulLongCS<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ const char *device=0;
|
|||
#include "device_cubin.h"
|
||||
#endif
|
||||
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define DeviceT Device<numtyp, acctyp>
|
||||
|
||||
template <class numtyp, class acctyp>
|
||||
|
|
@ -762,7 +762,9 @@ double DeviceT::host_memory_usage() const {
|
|||
|
||||
template class Device<PRECISION,ACC_PRECISION>;
|
||||
Device<PRECISION,ACC_PRECISION> global_device;
|
||||
}
|
||||
|
||||
using namespace LAMMPS_AL;
|
||||
int lmp_init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu,
|
||||
const int last_gpu, const int gpu_mode,
|
||||
const double particle_split, const int nthreads,
|
||||
|
|
@ -781,4 +783,3 @@ double lmp_gpu_forces(double **f, double **tor, double *eatom,
|
|||
double **vatom, double *virial, double &ecoul) {
|
||||
return global_device.fix_gpu(f,tor,eatom,vatom,virial,ecoul);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *dipole_lj=0;
|
|||
|
||||
#include "lal_dipole_lj.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define DipoleLJT DipoleLJ<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -168,3 +168,4 @@ void DipoleLJT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class DipoleLJ<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *dipole_lj_sf=0;
|
|||
|
||||
#include "lal_dipole_lj_sf.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define DipoleLJSFT DipoleLJSF<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -168,3 +168,4 @@ void DipoleLJSFT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class DipoleLJSF<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *dipole_long_lj=0;
|
|||
|
||||
#include "lal_dipole_long_lj.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define DipoleLongLJT DipoleLongLJ<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -171,3 +171,4 @@ void DipoleLongLJT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class DipoleLongLJ<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *dpd=0;
|
|||
|
||||
#include "lal_dpd.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define DPDT DPD<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -168,3 +168,4 @@ void DPDT::update_coeff(int ntypes, double **host_a0, double **host_gamma,
|
|||
}
|
||||
|
||||
template class DPD<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *eam=0;
|
|||
|
||||
#include "lal_eam.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define EAMT EAM<numtyp, acctyp>
|
||||
|
||||
|
||||
|
|
@ -531,3 +531,4 @@ void EAMT::loop2(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class EAM<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *gauss=0;
|
|||
|
||||
#include "lal_gauss.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define GaussT Gauss<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -159,3 +159,4 @@ void GaussT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Gauss<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ const char *gayberne_lj=0;
|
|||
|
||||
#include "lal_gayberne.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
#define GayBerneT GayBerne<numtyp, acctyp>
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -315,4 +315,4 @@ void GayBerneT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class GayBerne<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj=0;
|
|||
|
||||
#include "lal_lj.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJT LJ<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -168,3 +168,4 @@ void LJT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJ<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj96=0;
|
|||
|
||||
#include "lal_lj96.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJ96T LJ96<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -152,3 +152,4 @@ void LJ96T::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJ96<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -174,6 +174,7 @@ __kernel void k_lj96_fast(const __global numtyp4 *restrict x_,
|
|||
numtyp r6inv = r2inv*r2inv*r2inv;
|
||||
numtyp r3inv = ucl_sqrt(r6inv);
|
||||
numtyp force = r2inv*r6inv*(lj1[mtype].x*r3inv-lj1[mtype].y);
|
||||
force*=factor_lj;
|
||||
|
||||
f.x+=delx*force;
|
||||
f.y+=dely*force;
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_class2_long=0;
|
|||
|
||||
#include "lal_lj_class2_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
#define LJClass2LongT LJClass2Long<numtyp, acctyp>
|
||||
|
||||
|
|
@ -164,4 +164,4 @@ void LJClass2LongT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJClass2Long<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_coul=0;
|
|||
|
||||
#include "lal_lj_coul.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJCoulT LJCoul<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -164,3 +164,4 @@ void LJCoulT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJCoul<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_coul_debye=0;
|
|||
|
||||
#include "lal_lj_coul_debye.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJCoulDebyeT LJCoulDebye<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -166,3 +166,4 @@ void LJCoulDebyeT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJCoulDebye<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_coul_long=0;
|
|||
|
||||
#include "lal_lj_coul_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJCoulLongT LJCoulLong<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -181,3 +181,4 @@ void LJCoulLongT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJCoulLong<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_coul_msm=0;
|
|||
|
||||
#include "lal_lj_coul_msm.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJCoulMSMT LJCoulMSM<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -198,3 +198,4 @@ void LJCoulMSMT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJCoulMSM<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_cubic=0;
|
|||
|
||||
#include "lal_lj_cubic.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJCubicT LJCubic<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -157,3 +157,4 @@ void LJCubicT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJCubic<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_dsf=0;
|
|||
|
||||
#include "lal_lj_dsf.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJDSFT LJDSF<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -166,3 +166,4 @@ void LJDSFT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJDSF<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_expand=0;
|
|||
|
||||
#include "lal_lj_expand.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJExpandT LJExpand<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -171,3 +171,4 @@ void LJExpandT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJExpand<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_expand_coul_long=0;
|
|||
|
||||
#include "lal_lj_expand_coul_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJExpandCoulLongT LJExpandCoulLong<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -181,3 +181,4 @@ void LJExpandCoulLongT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJExpandCoulLong<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_gromacs=0;
|
|||
|
||||
#include "lal_lj_gromacs.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define LJGROMACST LJGROMACS<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -162,3 +162,4 @@ void LJGROMACST::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class LJGROMACS<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_sdk=0;
|
|||
|
||||
#include "lal_lj_sdk.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define CGCMMT CGCMM<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -152,3 +152,4 @@ void CGCMMT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class CGCMM<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *lj_sdk_long=0;
|
|||
|
||||
#include "lal_lj_sdk_long.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define CGCMMLongT CGCMMLong<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -164,3 +164,4 @@ void CGCMMLongT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class CGCMMLong<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *mie=0;
|
|||
|
||||
#include "lal_mie.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define MieT Mie<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -150,3 +150,4 @@ void MieT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Mie<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *morse=0;
|
|||
|
||||
#include "lal_morse.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define MorseT Morse<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -150,4 +150,4 @@ void MorseT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Morse<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@ const char *pppm_d=0;
|
|||
#include "lal_pppm.h"
|
||||
#include <cassert>
|
||||
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define PPPMT PPPM<numtyp, acctyp, grdtyp, grdtyp4>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> global_device;
|
||||
|
|
@ -402,3 +402,4 @@ void PPPMT::compile_kernels(UCL_Device &dev) {
|
|||
|
||||
template class PPPM<PRECISION,ACC_PRECISION,float,_lgpu_float4>;
|
||||
template class PPPM<PRECISION,ACC_PRECISION,double,_lgpu_double4>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ const char *re_squared_lj=0;
|
|||
|
||||
#include "lal_re_squared.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
|
||||
#define RESquaredT RESquared<numtyp, acctyp>
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -315,4 +315,4 @@ void RESquaredT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class RESquared<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *soft=0;
|
|||
|
||||
#include "lal_soft.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define SoftT Soft<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -158,3 +158,4 @@ void SoftT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Soft<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *sw=0;
|
|||
|
||||
#include "lal_sw.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define SWT SW<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -262,4 +262,4 @@ void SWT::loop(const bool _eflag, const bool _vflag, const int evatom) {
|
|||
}
|
||||
|
||||
template class SW<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *table=0;
|
|||
|
||||
#include "lal_table.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define TableT Table<numtyp, acctyp>
|
||||
|
||||
#define LOOKUP 0
|
||||
|
|
@ -337,3 +337,4 @@ void TableT::loop(const bool _eflag, const bool _vflag) {
|
|||
}
|
||||
|
||||
template class Table<PRECISION,ACC_PRECISION>;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *tersoff=0;
|
|||
|
||||
#include "lal_tersoff.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define TersoffT Tersoff<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -329,4 +329,4 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) {
|
|||
}
|
||||
|
||||
template class Tersoff<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -308,8 +308,6 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
|
|||
delr1.z = jx.z-ix.z;
|
||||
numtyp rsq1 = delr1.x*delr1.x+delr1.y*delr1.y+delr1.z*delr1.z;
|
||||
|
||||
// if (rsq1 > cutsq[ijparam]) continue;
|
||||
|
||||
// compute zeta_ij
|
||||
z = (acctyp)0;
|
||||
|
||||
|
|
@ -355,13 +353,9 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
|
|||
rsq1, rsq2, delr1, delr2);
|
||||
}
|
||||
|
||||
//int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride;
|
||||
//int idx = jj*n_stride + i*t_per_atom + offset_j;
|
||||
//idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
|
||||
int idx = nbor_j;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// i, nbor_j, offset_j, idx);
|
||||
acc_zeta(z, tid, t_per_atom, offset_k);
|
||||
|
||||
numtyp4 ts1_ijparam = ts1[ijparam]; //fetch4(ts1_ijparam,ijparam,ts1_tex);
|
||||
|
|
@ -585,14 +579,9 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_,
|
|||
numtyp r1inv = ucl_rsqrt(rsq1);
|
||||
|
||||
// look up for zeta_ij
|
||||
|
||||
//int jj = (nbor_j-offset_j-2*nbor_pitch) / n_stride;
|
||||
//int idx = jj*n_stride + i*t_per_atom + offset_j;
|
||||
//idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
|
||||
int idx = nbor_j;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// i, nbor_j, offset_j, idx);
|
||||
acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex);
|
||||
numtyp force = zeta_ij.x*tpainv;
|
||||
numtyp prefactor = zeta_ij.y;
|
||||
|
|
@ -823,13 +812,9 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
|
|||
offset_kf = red_acc[2*m+1];
|
||||
}
|
||||
|
||||
//int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
|
||||
//int idx = iix*n_stride + j*t_per_atom + offset_kf;
|
||||
//idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||
int idx = ijnum;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// j, ijnum, offset_kf, idx);
|
||||
acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
|
||||
numtyp force = zeta_ji.x*tpainv;
|
||||
numtyp prefactor_ji = zeta_ji.y;
|
||||
|
|
@ -891,13 +876,10 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
|
|||
f.y += fi[1];
|
||||
f.z += fi[2];
|
||||
|
||||
//int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
|
||||
//int idx = kk*n_stride + j*t_per_atom + offset_k;
|
||||
//idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
|
||||
int idx = nbor_k;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// j, nbor_k, offset_k, idx);
|
||||
|
||||
acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
|
||||
numtyp prefactor_jk = zeta_jk.y;
|
||||
int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
|
||||
|
|
@ -1068,13 +1050,9 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
|
|||
offset_kf = red_acc[2*m+1];
|
||||
}
|
||||
|
||||
//int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
|
||||
//int idx = iix*n_stride + j*t_per_atom + offset_kf;
|
||||
//idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||
int idx = ijnum;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// j, ijnum, offset_kf, idx);
|
||||
acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
|
||||
numtyp force = zeta_ji.x*tpainv;
|
||||
numtyp prefactor_ji = zeta_ji.y;
|
||||
|
|
@ -1143,13 +1121,9 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
|
|||
virial[4] += TWOTHIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]);
|
||||
virial[5] += TWOTHIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]);
|
||||
|
||||
//int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
|
||||
//int idx = kk*n_stride + j*t_per_atom + offset_k;
|
||||
//idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
|
||||
int idx = nbor_k;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// j, nbor_k, offset_k, idx);
|
||||
acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
|
||||
numtyp prefactor_jk = zeta_jk.y;
|
||||
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ const char *tersoff_mod=0;
|
|||
|
||||
#include "lal_tersoff_mod.h"
|
||||
#include <cassert>
|
||||
using namespace LAMMPS_AL;
|
||||
namespace LAMMPS_AL {
|
||||
#define TersoffMT TersoffMod<numtyp, acctyp>
|
||||
|
||||
extern Device<PRECISION,ACC_PRECISION> device;
|
||||
|
|
@ -329,4 +329,4 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) {
|
|||
}
|
||||
|
||||
template class TersoffMod<PRECISION,ACC_PRECISION>;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -356,13 +356,9 @@ __kernel void k_tersoff_mod_zeta(const __global numtyp4 *restrict x_,
|
|||
ijkparam_c5, rsq1, rsq2, delr1, delr2);
|
||||
}
|
||||
|
||||
//int jj = (nbor_j-offset_j-2*nbor_pitch)/n_stride;
|
||||
//int idx = jj*n_stride + i*t_per_atom + offset_j;
|
||||
//idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
|
||||
int idx = nbor_j;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// i, nbor_j, offset_j, idx);
|
||||
acc_zeta(z, tid, t_per_atom, offset_k);
|
||||
|
||||
numtyp4 ts1_ijparam = ts1[ijparam]; //fetch4(ts1_ijparam,ijparam,ts1_tex);
|
||||
|
|
@ -587,14 +583,9 @@ __kernel void k_tersoff_mod_three_center(const __global numtyp4 *restrict x_,
|
|||
numtyp r1inv = ucl_rsqrt(rsq1);
|
||||
|
||||
// look up for zeta_ij
|
||||
|
||||
//int jj = (nbor_j-offset_j-2*nbor_pitch) / n_stride;
|
||||
//int idx = jj*n_stride + i*t_per_atom + offset_j;
|
||||
//idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to nbor_j in dev_short_nbor
|
||||
int idx = nbor_j;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// i, nbor_j, offset_j, idx);
|
||||
acctyp4 zeta_ij = zetaij[idx]; // fetch(zeta_ij,idx,zeta_tex);
|
||||
numtyp force = zeta_ij.x*tpainv;
|
||||
numtyp prefactor = zeta_ij.y;
|
||||
|
|
@ -831,13 +822,9 @@ __kernel void k_tersoff_mod_three_end(const __global numtyp4 *restrict x_,
|
|||
offset_kf = red_acc[2*m+1];
|
||||
}
|
||||
|
||||
//int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
|
||||
//int idx = iix*n_stride + j*t_per_atom + offset_kf;
|
||||
//idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||
int idx = ijnum;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// j, ijnum, offset_kf, idx);
|
||||
acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
|
||||
numtyp force = zeta_ji.x*tpainv;
|
||||
numtyp prefactor_ji = zeta_ji.y;
|
||||
|
|
@ -902,13 +889,9 @@ __kernel void k_tersoff_mod_three_end(const __global numtyp4 *restrict x_,
|
|||
f.y += fi[1];
|
||||
f.z += fi[2];
|
||||
|
||||
//int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
|
||||
//int idx = kk*n_stride + j*t_per_atom + offset_k;
|
||||
//idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
|
||||
int idx = nbor_k;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// j, nbor_k, offset_k, idx);
|
||||
acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
|
||||
numtyp prefactor_jk = zeta_jk.y;
|
||||
int jkiparam=elem2param[jtype*nelements*nelements+ktype*nelements+itype];
|
||||
|
|
@ -1085,13 +1068,9 @@ __kernel void k_tersoff_mod_three_end_vatom(const __global numtyp4 *restrict x_,
|
|||
offset_kf = red_acc[2*m+1];
|
||||
}
|
||||
|
||||
//int iix = (ijnum - offset_kf - 2*nbor_pitch) / n_stride;
|
||||
//int idx = iix*n_stride + j*t_per_atom + offset_kf;
|
||||
//idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||
int idx = ijnum;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// j, ijnum, offset_kf, idx);
|
||||
acctyp4 zeta_ji = zetaij[idx]; // fetch(zeta_ji,idx,zeta_tex);
|
||||
numtyp force = zeta_ji.x*tpainv;
|
||||
numtyp prefactor_ji = zeta_ji.y;
|
||||
|
|
@ -1163,13 +1142,9 @@ __kernel void k_tersoff_mod_three_end_vatom(const __global numtyp4 *restrict x_,
|
|||
virial[4] += TWOTHIRD*(mdelr1[0]*fj[2] + delr2[0]*fk[2]);
|
||||
virial[5] += TWOTHIRD*(mdelr1[1]*fj[2] + delr2[1]*fk[2]);
|
||||
|
||||
//int kk = (nbor_k - offset_k - 2*nbor_pitch) / n_stride;
|
||||
//int idx = kk*n_stride + j*t_per_atom + offset_k;
|
||||
//idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
|
||||
// idx to zetaij is shifted by n_stride relative to nbor_k in dev_short_nbor
|
||||
int idx = nbor_k;
|
||||
if (dev_packed==dev_nbor) idx -= n_stride;
|
||||
// zeta_idx(dev_nbor,dev_packed, nbor_pitch, n_stride, t_per_atom,
|
||||
// j, nbor_k, offset_k, idx);
|
||||
acctyp4 zeta_jk = zetaij[idx]; // fetch(zeta_jk,idx,zeta_tex);
|
||||
numtyp prefactor_jk = zeta_jk.y;
|
||||
|
||||
|
|
|
|||
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Reference in New Issue