Merge branch 'master' into feature-cnt
This commit is contained in:
iafoss
@ -1845,7 +1845,7 @@ Translation force removed: ( -0.00000 -0.00000 -0.00000)
|
||||
|
||||
|
||||
|
||||
Outputing formatted_stress_filename: ./W.vpp2
|
||||
Outputting formatted_stress_filename: ./W.vpp2
|
||||
|
||||
|
||||
======================
|
||||
|
||||
@ -84,7 +84,7 @@ int main(int narg, char **arg)
|
||||
|
||||
lmp->input->file(lammps_input);
|
||||
|
||||
// make info avaiable to callback function
|
||||
// make info available to callback function
|
||||
|
||||
Info info;
|
||||
info.me = me;
|
||||
|
||||
@ -6,7 +6,7 @@ All input scripts are part of the supplementary (open access) material
|
||||
supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143,
|
||||
124104 (2015)] and allow one to reproduce the key results reported in
|
||||
that paper. The full article is available for download under
|
||||
http://dx.doi.org/10.1063/1.4931597 or http://arxiv.org/pdf/1507.07081
|
||||
https://doi.org/10.1063/1.4931597 or http://arxiv.org/pdf/1507.07081
|
||||
and the supplementary material is available under
|
||||
https://www.repository.cam.ac.uk/handle/1810/250539.
|
||||
|
||||
|
||||
@ -27,7 +27,7 @@ The real and metal scripts each have a set of variables at the top
|
||||
which define scale factors for converting quantities like distance,
|
||||
energy, pressure from reduced LJ units to real or metal units. Once
|
||||
these are defined the rest of the input script is very similar to the
|
||||
LJ script. The approprate scale factor is applied to every input.
|
||||
LJ script. The appropriate scale factor is applied to every input.
|
||||
Output quantities are printed in both the native real/metal units and
|
||||
unscaled back to LJ units. So that you can see the outputs are the
|
||||
same if you examine the log files. Comments about this comparison
|
||||
@ -49,6 +49,6 @@ identical input script in an alternate set of units. Where
|
||||
"identical" means it runs the same simulation in a statistical sense.
|
||||
|
||||
You can find the full set of scale factors LAMMPS uses internally for
|
||||
different unit systems it supports, at the top of the src/udpate.cpp
|
||||
different unit systems it supports, at the top of the src/update.cpp
|
||||
file. A couple of those values are used in the real and metal
|
||||
scripts.
|
||||
|
||||
@ -68,7 +68,7 @@ elastic:
|
||||
in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field
|
||||
in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field
|
||||
in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold
|
||||
in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field
|
||||
in.electron_density - Mechanical response of different CNT models with a self-consistent electron density and electric field
|
||||
in.electrostatic_bending_dos - Quasi-static bending of a CNT using a quantum density of states model for electron density
|
||||
in.no_atoms - FE solution of a box subject to an initial displacement condition
|
||||
in.no_atoms_cb - FE solution of a box subject to an initial displacement condition with a Cauchy-Born material model
|
||||
@ -149,7 +149,7 @@ elastic:
|
||||
in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field
|
||||
in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field
|
||||
in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold
|
||||
in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field
|
||||
in.electron_density - Mechanical response of different CNT models with a self-consistent electron density and electric field
|
||||
in.electrostatic_bending_dos - Quasi-static bending of a CNT using a quantum density of states model for electron density
|
||||
in.no_atoms - FE solution of a box subject to an initial displacement condition
|
||||
in.no_atoms_cb - FE solution of a box subject to an initial displacement condition with a Cauchy-Born material model
|
||||
|
||||
@ -85,7 +85,7 @@ fix_modify AtC control localized_lambda on
|
||||
fix_modify AtC filter type exponential
|
||||
fix_modify AtC filter scale 1000.0
|
||||
fix_modify AtC filter on
|
||||
# ouput commands
|
||||
# output commands
|
||||
fix_modify AtC output bar1d_fluidsFE 100 text
|
||||
#undump D1
|
||||
#dump D2 all atom 200 dump.bar1d
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
# simulation of negatively charge liquid argon-positively charged solid/frozen argon
|
||||
# MAKE this conducting_interface then interface (major difference: non-uniform grid)
|
||||
# START with extrinsic charges on both and then use an instrinsic charge density for frozen
|
||||
# START with extrinsic charges on both and then use an intrinsic charge density for frozen
|
||||
echo both
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
# simulation of negatively charge liquid argon-positively charged solid/frozen argon
|
||||
# MAKE this dielectric_interface then interface (major difference: non-uniform grid)
|
||||
# START with extrinsic charges on both and then use an instrinsic charge density for frozen
|
||||
# START with extrinsic charges on both and then use an intrinsic charge density for frozen
|
||||
echo both
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
@ -75,7 +75,7 @@ fix_modify AtC control localized_lambda on
|
||||
#fix_modify AtC filter scale 1000.0
|
||||
#fix_modify AtC filter on
|
||||
|
||||
# ouput commands
|
||||
# output commands
|
||||
fix_modify AtC output shear_flowFE 100 text #binary
|
||||
#undump D1
|
||||
#dump D1 all custom 100 shear_flow.dmp id type xs ys zs vx vy vz
|
||||
|
||||
@ -25,7 +25,7 @@ fix_modify AtC reset_time
|
||||
fix_modify AtC fix velocity y rbc 0.1
|
||||
fix_modify AtC fix velocity y lbc 0.
|
||||
|
||||
# ouput commands
|
||||
# output commands
|
||||
fix_modify AtC output shear_no_atomsFE 200 text binary
|
||||
# set-up non-equilibrium IC
|
||||
thermo 100
|
||||
|
||||
@ -239,7 +239,7 @@ fix_modify AtC output bar1dFE 100 text binary
|
||||
ATC: Warning : text output can create _LARGE_ files
|
||||
ATC: output custom names:
|
||||
|
||||
# ouput command
|
||||
# output command
|
||||
#dump D1 all atom 1000 dump.bar1d
|
||||
# run with FE
|
||||
reset_timestep 0
|
||||
|
||||
@ -71,7 +71,7 @@ thermo 1
|
||||
run 100
|
||||
# set up output, should be before a "run"
|
||||
fix_modify AtC output bar1dFE 100 text binary
|
||||
# ouput command
|
||||
# output command
|
||||
#dump D1 all atom 1000 dump.bar1d
|
||||
# run with FE
|
||||
reset_timestep 0
|
||||
|
||||
@ -93,7 +93,7 @@ fix_modify AtC fix_flux temperature lbndy 0.0000000001
|
||||
fix_modify AtC fix_flux temperature rbndy -0.0000000001
|
||||
# set up output, should be before a "run"
|
||||
fix_modify AtC output bar1d_all_atomsFE 200 text binary
|
||||
# ouput command
|
||||
# output command
|
||||
#dump D1 all atom 1000 dump.bar1d
|
||||
# run with FE
|
||||
reset_timestep 0
|
||||
|
||||
@ -79,7 +79,7 @@ thermo 100
|
||||
|
||||
# set up output, should be before a "run"
|
||||
fix_modify AtC output bar1d_combinedFE 100 text
|
||||
# ouput command
|
||||
# output command
|
||||
#dump D1 all atom 100 dump.bar1d_combined
|
||||
# run with FE
|
||||
reset_timestep 0
|
||||
|
||||
@ -71,7 +71,7 @@ fix_modify AtC fix temperature rbc 20.
|
||||
run 100
|
||||
# set up output, should be before a "run"
|
||||
fix_modify AtC output bar1d_fluxFE 100 text binary
|
||||
# ouput command
|
||||
# output command
|
||||
#dump D1 all atom 1000 dump.bar1d
|
||||
# run with FE
|
||||
reset_timestep 0
|
||||
|
||||
@ -72,7 +72,7 @@ fix_modify AtC filter scale 1000.0
|
||||
fix_modify AtC filter on
|
||||
# set up output, should be before a "run"
|
||||
fix_modify AtC output bar1d_frac_stepFE 200 text
|
||||
# ouput command
|
||||
# output command
|
||||
#dump D1 all atom 1000 dump.bar1d
|
||||
# run with FE
|
||||
reset_timestep 0
|
||||
|
||||
@ -46,7 +46,7 @@ moment of inertia set to the value used in the standalone implementation
|
||||
of oxDNA (M = I = 1). 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
|
||||
The change of mass and moment of inertia allows direct comparison of
|
||||
trajectory data or time-dependent observables on a per-timestep basis.
|
||||
|
||||
As mentioned above, the stacking and hydrogen-bonding interactions
|
||||
|
||||
@ -105,7 +105,7 @@ EXCL_RC2 = 0.335388426126
|
||||
EXCL_RC3 = 0.52329943261
|
||||
|
||||
"""
|
||||
Define auxillary variables for the construction of a helix
|
||||
Define auxiliary variables for the construction of a helix
|
||||
"""
|
||||
# center of the double strand
|
||||
COM_CENTRE_DS = POS_BASE + 0.2
|
||||
@ -127,7 +127,7 @@ number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'}
|
||||
base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2,
|
||||
'G' : 3, 'g' : 3, 'T' : 4, 't' : 4}
|
||||
|
||||
# auxillary arrays
|
||||
# auxiliary arrays
|
||||
positions = []
|
||||
a1s = []
|
||||
a3s = []
|
||||
@ -373,7 +373,7 @@ def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
|
||||
# if not provided switch off random orientation
|
||||
if perp is None or perp is False:
|
||||
v1 = np.random.random_sample(3)
|
||||
# comment in to suppress randomised base vector
|
||||
# comment in to suppress randomized base vector
|
||||
v1 = [1,0,0]
|
||||
v1 -= dir * (np.dot(dir, v1))
|
||||
v1 /= np.sqrt(sum(v1*v1))
|
||||
@ -551,7 +551,7 @@ def read_strands(filename):
|
||||
smallest_n_bases = n_g
|
||||
|
||||
if smallest_n_bases < N_BASE_TYPES:
|
||||
print('## Not enough occurances of base types in the sequence for ' + str(N_BASE_TYPES))
|
||||
print('## Not enough occurrences of base types in the sequence for ' + str(N_BASE_TYPES))
|
||||
print('## unique base types, switching to ' + str(smallest_n_bases) + ' unique types')
|
||||
else:
|
||||
smallest_n_bases = N_BASE_TYPES
|
||||
@ -644,12 +644,12 @@ def read_strands(filename):
|
||||
|
||||
# generate random position of the first nucleotide
|
||||
com = box_offset + np.random.random_sample(3) * box
|
||||
# comment out to randomise
|
||||
# comment out to randomize
|
||||
com = [0,0,0]
|
||||
|
||||
# generate the random direction of the helix
|
||||
axis = np.random.random_sample(3)
|
||||
# comment out to randomise
|
||||
# comment out to randomize
|
||||
axis = [0,0,1]
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
|
||||
@ -702,12 +702,12 @@ def read_strands(filename):
|
||||
|
||||
# generate random position of the first nucleotide
|
||||
com = box_offset + np.random.random_sample(3) * box
|
||||
# comment out to randomise
|
||||
# comment out to randomize
|
||||
com = [-30,0,0]
|
||||
|
||||
# generate the random direction of the helix
|
||||
axis = np.random.random_sample(3)
|
||||
# comment out to randomise
|
||||
# comment out to randomize
|
||||
axis = [0,0,1]
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@ EXCL_RC2 = 0.335388426126
|
||||
EXCL_RC3 = 0.52329943261
|
||||
|
||||
"""
|
||||
Define auxillary variables for the construction of a helix
|
||||
Define auxiliary variables for the construction of a helix
|
||||
"""
|
||||
# center of the double strand
|
||||
CM_CENTER_DS = POS_BASE + 0.2
|
||||
@ -103,7 +103,7 @@ number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'}
|
||||
base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2,
|
||||
'G' : 3, 'g' : 3, 'T' : 4, 't' : 4}
|
||||
|
||||
# auxillary arrays
|
||||
# auxiliary arrays
|
||||
positions = []
|
||||
a1s = []
|
||||
a3s = []
|
||||
|
||||
@ -101,7 +101,7 @@ colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
@ -405,7 +405,7 @@ colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
|
||||
@ -101,7 +101,7 @@ colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
@ -405,7 +405,7 @@ colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
|
||||
@ -100,7 +100,7 @@ colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
|
||||
@ -100,7 +100,7 @@ colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: http://dx.doi.org/10.1080/00268976.2013.813594
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
This is a simple example of showing the computation of virutal x-ray
|
||||
This is a simple example of showing the computation of virtual x-ray
|
||||
and electron diffraction patterns for Ni.
|
||||
|
||||
In addition to the LAMMPS output, a simple visualizaiton of the electron
|
||||
|
||||
@ -1,2 +1,2 @@
|
||||
Shows the formation of lithium dendrites during the minimization of a volume expanded lithium cell with particle positions remaped to fit the cell.
|
||||
Shows the formation of lithium dendrites during the minimization of a volume expanded lithium cell with particle positions remapped to fit the cell.
|
||||
This depicts the process of electrode replating in lithium batteries, which leads to failure (short-circuit).
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
#===========================================================================#
|
||||
# Sytem of 2 pairs of rigid particles moving towards one another. #
|
||||
# System of 2 pairs of rigid particles moving towards one another. #
|
||||
# At each timestep, the hydrodynamic force acting on one of these four #
|
||||
# rigid particles is printed to the screen. #
|
||||
# #
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
#===========================================================================#
|
||||
# Sytem of 2 pairs of rigid particles moving towards one another. #
|
||||
# System of 2 pairs of rigid particles moving towards one another. #
|
||||
# At each timestep, the hydrodynamic force acting on one of these four #
|
||||
# rigid particles is printed to the screen. #
|
||||
# #
|
||||
|
||||
@ -47,7 +47,7 @@ set object 1 rectangle from graph 0,0 to graph 1,1 fillcolor rgb "white" behind
|
||||
unset key
|
||||
set grid front
|
||||
|
||||
set title 'Short time behaviour' offset 0,-0.8
|
||||
set title 'Short time behavior' offset 0,-0.8
|
||||
set ylabel ''
|
||||
set xrange[0:10]
|
||||
set yrange[0:40]
|
||||
|
||||
@ -5,7 +5,7 @@ Here one may find simple examples showing how "fix wall/ess" and "fix wall/regio
|
||||
|
||||
This input uses "Data_region" to setup a system of three particles colliding with a
|
||||
cubic region which its walls interact with particle with EES potential. To find out details
|
||||
of how to set parameters of "fix wall/region/ees" see documentaion.
|
||||
of how to set parameters of "fix wall/region/ees" see documentation.
|
||||
|
||||
--in.fix_wall
|
||||
|
||||
|
||||
@ -15,7 +15,7 @@ Averages of the potential energy (#3 and #4) agree although #4 (HMA) is more pre
|
||||
Averages of the pressure (#5 and #6) agree once the ideal gas
|
||||
contribution is included; #6 (HMA) is more precise.
|
||||
|
||||
The heat capacity can be computed from colume #3 (convential) as
|
||||
The heat capacity can be computed from colume #3 (conventional) as
|
||||
Cv = Var(#3)/(k T^2)
|
||||
|
||||
With HMA, the heat capacity can be computed from column #4 and #7 as
|
||||
|
||||
@ -19,7 +19,7 @@ For future reference we note that the structure factor S(k) is given by the vari
|
||||
|
||||
It is recommended to get familiar with the interface pinning method by reading:
|
||||
|
||||
[Ulf R. Pedersen, JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747)
|
||||
[Ulf R. Pedersen, JCP 139, 104102 (2013)](https://doi.org/10.1063/1.4818747)
|
||||
|
||||
A detailed bibliography is provided at
|
||||
|
||||
@ -63,8 +63,8 @@ can be used to show this. The present directory contains the input files that we
|
||||
the value fluctuates around the anchor point (a) -- showing that this is indeed a coexistence
|
||||
state point.
|
||||
|
||||
The reference [JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points,
|
||||
and the reference [JCP 142, 044104 (2015)](http://dx.doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations.
|
||||
The reference [JCP 139, 104102 (2013)](https://doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points,
|
||||
and the reference [JCP 142, 044104 (2015)](https://doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations.
|
||||
That method have been experienced to be most effective in the slightly super-heated regime above the melting temperature.
|
||||
|
||||
## Contact
|
||||
|
||||
6020
examples/USER/misc/slater/data.after_equilibration
Normal file
6020
examples/USER/misc/slater/data.after_equilibration
Normal file
File diff suppressed because it is too large
Load Diff
6020
examples/USER/misc/slater/data.after_production_run
Normal file
6020
examples/USER/misc/slater/data.after_production_run
Normal file
File diff suppressed because it is too large
Load Diff
60
examples/USER/misc/slater/in.slater
Normal file
60
examples/USER/misc/slater/in.slater
Normal file
@ -0,0 +1,60 @@
|
||||
# Bulk polyelectrolyte as described in section IV of J. Chem. Phys. 125, 224107 (2006)
|
||||
|
||||
boundary p p p
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
|
||||
region my_sim_box block 0.0 10.0 0.0 10.0 0.0 10.0
|
||||
create_box 3 my_sim_box
|
||||
|
||||
create_atoms 1 random 2804 100 my_sim_box
|
||||
create_atoms 2 random 98 200 my_sim_box
|
||||
create_atoms 3 random 98 300 my_sim_box
|
||||
|
||||
set type 2 charge -1.0
|
||||
set type 3 charge 1.0
|
||||
|
||||
comm_modify mode single vel yes
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
pair_style hybrid/overlay dpd 1.0 1.0 245455 coul/slater/long 0.929 3.0
|
||||
pair_coeff * * dpd 25.0 4.5
|
||||
pair_coeff * * coul/slater/long
|
||||
|
||||
kspace_style ewald 0.00001
|
||||
dielectric 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check no once no
|
||||
|
||||
timestep 0.02
|
||||
|
||||
fix 2 all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step spcpu temp press etotal pe ke ecoul elong evdwl
|
||||
thermo_modify line one
|
||||
|
||||
run 100000
|
||||
write_data data.after_equilibration
|
||||
|
||||
compute RDF_1_1 all rdf 50 1 1 cutoff 3.0
|
||||
compute RDF_1_2 all rdf 50 1 2 cutoff 3.0
|
||||
compute RDF_1_3 all rdf 50 1 3 cutoff 3.0
|
||||
compute RDF_2_2 all rdf 50 2 2 cutoff 3.0
|
||||
compute RDF_2_3 all rdf 50 2 3 cutoff 3.0
|
||||
compute RDF_3_3 all rdf 50 3 3 cutoff 3.0
|
||||
|
||||
fix 11 all ave/time 50 1 50 c_RDF_1_1[*] file tmp_1_1.rdf mode vector
|
||||
fix 12 all ave/time 50 1 50 c_RDF_1_2[*] file tmp_1_2.rdf mode vector
|
||||
fix 13 all ave/time 50 1 50 c_RDF_1_3[*] file tmp_1_3.rdf mode vector
|
||||
fix 14 all ave/time 50 1 50 c_RDF_2_2[*] file tmp_2_2.rdf mode vector
|
||||
fix 15 all ave/time 50 1 50 c_RDF_2_3[*] file tmp_2_3.rdf mode vector
|
||||
fix 16 all ave/time 50 1 50 c_RDF_3_3[*] file tmp_3_3.rdf mode vector
|
||||
|
||||
run 10000
|
||||
write_data data.after_production_run
|
||||
11225
examples/USER/misc/slater/log.lammps
Normal file
11225
examples/USER/misc/slater/log.lammps
Normal file
File diff suppressed because it is too large
Load Diff
10254
examples/USER/misc/slater/tmp_1_1.rdf
Normal file
10254
examples/USER/misc/slater/tmp_1_1.rdf
Normal file
File diff suppressed because it is too large
Load Diff
10254
examples/USER/misc/slater/tmp_1_2.rdf
Normal file
10254
examples/USER/misc/slater/tmp_1_2.rdf
Normal file
File diff suppressed because it is too large
Load Diff
10254
examples/USER/misc/slater/tmp_1_3.rdf
Normal file
10254
examples/USER/misc/slater/tmp_1_3.rdf
Normal file
File diff suppressed because it is too large
Load Diff
10254
examples/USER/misc/slater/tmp_2_2.rdf
Normal file
10254
examples/USER/misc/slater/tmp_2_2.rdf
Normal file
File diff suppressed because it is too large
Load Diff
10254
examples/USER/misc/slater/tmp_2_3.rdf
Normal file
10254
examples/USER/misc/slater/tmp_2_3.rdf
Normal file
File diff suppressed because it is too large
Load Diff
10254
examples/USER/misc/slater/tmp_3_3.rdf
Normal file
10254
examples/USER/misc/slater/tmp_3_3.rdf
Normal file
File diff suppressed because it is too large
Load Diff
@ -2,7 +2,7 @@
|
||||
#
|
||||
# Description: nonequilibrium thermodynamic integration. Further details in:
|
||||
# R. Freitas, M. Asta, and M. de Koning, Computational Materials Science, (2016)
|
||||
# http://dx.doi.org/10.1016/j.commatsci.2015.10.050
|
||||
# https://doi.org/10.1016/j.commatsci.2015.10.050
|
||||
|
||||
|
||||
#--------------------------- System setup -------------------------------------#
|
||||
|
||||
@ -48,7 +48,7 @@ PLUMED: [1] The PLUMED consortium, Nat. Methods 16, 670 (2019)
|
||||
PLUMED: [2] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
|
||||
PLUMED: Please read and cite where appropriate!
|
||||
PLUMED: Finished setup
|
||||
PLUMED: Cycles Total Average Minumum Maximum
|
||||
PLUMED: Cycles Total Average Minimum Maximum
|
||||
PLUMED: 1 0.010018 0.010018 0.010018 0.010018
|
||||
PLUMED: 1 Prepare dependencies 102 0.000241 0.000002 0.000001 0.000003
|
||||
PLUMED: 2 Sharing data 102 0.002132 0.000021 0.000006 0.000151
|
||||
|
||||
@ -48,7 +48,7 @@ neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initilization
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
|
||||
@ -54,7 +54,7 @@ neigh_modify every 10 delay 0 check no
|
||||
|
||||
|
||||
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
|
||||
#Initilization
|
||||
#Initialization
|
||||
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
|
||||
|
||||
#Setup output
|
||||
|
||||
@ -17,7 +17,7 @@ pair_style hybrid/overlay lj/cut 8.0 quip
|
||||
special_bonds lj/coul 0.999999999 0.999999999 0.999999999
|
||||
|
||||
# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
|
||||
# Coulomb interactions ommitted for simplicity
|
||||
# Coulomb interactions omitted for simplicity
|
||||
pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
|
||||
pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
|
||||
pair_coeff 1 2 lj/cut 0.0019295487 2.95
|
||||
|
||||
@ -39,7 +39,7 @@ special_bonds lj/coul 0.999999999 0.999999999 0.999999999
|
||||
4 = max # of special neighbors
|
||||
|
||||
# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
|
||||
# Coulomb interactions ommitted for simplicity
|
||||
# Coulomb interactions omitted for simplicity
|
||||
pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
|
||||
pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
|
||||
pair_coeff 1 2 lj/cut 0.0019295487 2.95
|
||||
|
||||
@ -39,7 +39,7 @@ special_bonds lj/coul 0.999999999 0.999999999 0.999999999
|
||||
4 = max # of special neighbors
|
||||
|
||||
# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
|
||||
# Coulomb interactions ommitted for simplicity
|
||||
# Coulomb interactions omitted for simplicity
|
||||
pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
|
||||
pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
|
||||
pair_coeff 1 2 lj/cut 0.0019295487 2.95
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
#
|
||||
# TLSPH example: elongate a 2d strip of aluminum py pulling its ends apart
|
||||
#
|
||||
# unit sytem: GPa / mm / ms
|
||||
# unit system: GPa / mm / ms
|
||||
#
|
||||
####################################################################################################
|
||||
|
||||
@ -18,7 +18,7 @@ variable q2 equal 0.0 # standard artificial viscosity quadratic coeffici
|
||||
variable hg equal 10.0 # hourglass control coefficient
|
||||
variable cp equal 1.0 # heat capacity of material -- not used here
|
||||
|
||||
variable JC_A equal 0.3241 # Johnson Cook arameters
|
||||
variable JC_A equal 0.3241 # Johnson Cook parameters
|
||||
variable JC_B equal 0.1138
|
||||
variable JC_N equal 0.42
|
||||
variable JC_C equal 0 #0.002
|
||||
|
||||
@ -4,7 +4,7 @@
|
||||
#
|
||||
# A column of water is placed in a container and allowed to collapse unter the
|
||||
# influence of gravity. Several solid objects are also placed in the container.
|
||||
# The water flow pushes the solid objects around until the sytem comes to halt due to
|
||||
# The water flow pushes the solid objects around until the system comes to halt due to
|
||||
# viscous damping. The solid objects have a lower mass density than water and finally float on
|
||||
# the water surface.
|
||||
#
|
||||
@ -12,7 +12,7 @@
|
||||
# Total Lagrangian formalism. Contact forces between container, solid bodies, and water prevent
|
||||
# mutual penetration of these physical entities.
|
||||
#
|
||||
# unit sytem: GPa / mm / ms
|
||||
# unit system: GPa / mm / ms
|
||||
#
|
||||
####################################################################################################
|
||||
|
||||
|
||||
@ -5,7 +5,7 @@
|
||||
# The boundary dump file (see below) can be converted into VTK format using the conversion
|
||||
# tool dump2vtk_tris from the tools/smd directory.
|
||||
#
|
||||
# unit sytem: GPa / mm / ms
|
||||
# unit system: GPa / mm / ms
|
||||
#
|
||||
####################################################################################################
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
#
|
||||
# TLSPH example: Two rubber rings impact each other.
|
||||
#
|
||||
# unit sytem: GPa / mm / ms
|
||||
# unit system: GPa / mm / ms
|
||||
#
|
||||
####################################################################################################
|
||||
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
#
|
||||
# TLSPH example: elongate a 2d strip of a linear elastic material py pulling its ends apart
|
||||
#
|
||||
# unit sytem: GPa / mm / ms
|
||||
# unit system: GPa / mm / ms
|
||||
#
|
||||
####################################################################################################
|
||||
|
||||
|
||||
@ -37,7 +37,7 @@ group hyd type 2
|
||||
compute epa oxy group/group hyd pair yes kspace no boundary no
|
||||
# tally pairwise energy between all oygen and all hydrogen
|
||||
compute c1 oxy pe/tally hyd
|
||||
# tally pairwise energy beween all atoms to compare with globals
|
||||
# tally pairwise energy between all atoms to compare with globals
|
||||
compute c2 all pe/tally all
|
||||
# collect per atom energies
|
||||
compute c3 all pe/atom pair
|
||||
|
||||
@ -89,7 +89,7 @@ group hyd type 2
|
||||
compute epa oxy group/group hyd pair yes kspace no boundary no
|
||||
# tally pairwise energy between all oygen and all hydrogen
|
||||
compute c1 oxy pe/tally hyd
|
||||
# tally pairwise energy beween all atoms to compare with globals
|
||||
# tally pairwise energy between all atoms to compare with globals
|
||||
compute c2 all pe/tally all
|
||||
# collect per atom energies
|
||||
compute c3 all pe/atom pair
|
||||
|
||||
@ -89,7 +89,7 @@ group hyd type 2
|
||||
compute epa oxy group/group hyd pair yes kspace no boundary no
|
||||
# tally pairwise energy between all oygen and all hydrogen
|
||||
compute c1 oxy pe/tally hyd
|
||||
# tally pairwise energy beween all atoms to compare with globals
|
||||
# tally pairwise energy between all atoms to compare with globals
|
||||
compute c2 all pe/tally all
|
||||
# collect per atom energies
|
||||
compute c3 all pe/atom pair
|
||||
|
||||
@ -67,7 +67,7 @@ fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to ouput etotal
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
@ -115,7 +115,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to ouput etotal
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
@ -153,7 +153,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to ouput etotal
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
|
||||
@ -129,7 +129,7 @@ fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to ouput etotal
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
@ -232,7 +232,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to ouput etotal
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
@ -327,7 +327,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to ouput etotal
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
|
||||
@ -129,7 +129,7 @@ fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to ouput etotal
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
@ -232,7 +232,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to ouput etotal
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
@ -327,7 +327,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
|
||||
|
||||
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
|
||||
|
||||
# Add fix energy to ouput etotal
|
||||
# Add fix energy to output etotal
|
||||
|
||||
fix_modify myhug energy yes
|
||||
|
||||
|
||||
13
examples/numdiff/README.md
Normal file
13
examples/numdiff/README.md
Normal file
@ -0,0 +1,13 @@
|
||||
# LAMMPS FIX NUMDIFF EXAMPLE
|
||||
|
||||
## Numerical Difference Fix
|
||||
|
||||
This directory contains the ingredients to run an NVE simulation using the numerical difference fix and calculate error in forces.
|
||||
|
||||
Example:
|
||||
```
|
||||
NP=4 #number of processors
|
||||
mpirun -np $NP lmp_mpi -in.numdiff
|
||||
```
|
||||
|
||||
## Required LAMMPS packages: MOLECULE package
|
||||
33
examples/numdiff/in.numdiff
Normal file
33
examples/numdiff/in.numdiff
Normal file
@ -0,0 +1,33 @@
|
||||
# Numerical difference calculation of error in forces
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
atom_modify map yes
|
||||
lattice fcc 5.358000
|
||||
region box block 0 6 0 6 0 6
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 39.903
|
||||
|
||||
velocity all create 10 2357 mom yes dist gaussian
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 0.0102701 3.42
|
||||
|
||||
neighbor 1 bin
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix numdiff all numdiff 200 0.0001
|
||||
fix nve all nve
|
||||
|
||||
variable errx atom fx-f_numdiff[1]
|
||||
variable erry atom fy-f_numdiff[2]
|
||||
variable errz atom fz-f_numdiff[3]
|
||||
|
||||
write_dump all custom tmp.error f_numdiff[1] f_numdiff[2] f_numdiff[3]
|
||||
|
||||
dump forces all custom 200 force_error.dump v_errx v_erry v_errz
|
||||
thermo 200
|
||||
run 2000
|
||||
@ -17,7 +17,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov
|
||||
The type of simulation is set by the 'fix' commands, dynamic charges are controlled with 'fix qeq' and the integration style is given as 'fix nve' here.
|
||||
More information about each of the individual commands can be found online at lammps.sandia.gov in the user manual section.
|
||||
|
||||
*There are four free varaibles in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken.
|
||||
*There are four free variables in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken.
|
||||
*The size of the system is controlled by the 'replicate' command given the values of $x, $y and $z.
|
||||
*The number of timesteps taken is controlled by the 'run' command given the value of $t
|
||||
|
||||
|
||||
Reference in New Issue
Block a user