Merge pull request #4095 from robeme/electrode
Update for the ELECTRODE package
This commit is contained in:
Axel Kohlmeyer
@ -45,7 +45,7 @@ Syntax
|
|||||||
rng_v = integer used to initialize random number generator
|
rng_v = integer used to initialize random number generator
|
||||||
|
|
||||||
* zero or more keyword/value pairs may be appended
|
* zero or more keyword/value pairs may be appended
|
||||||
* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
|
* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* or *qtotal* or *eta*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -68,6 +68,10 @@ Syntax
|
|||||||
filename = file from which to read elastance matrix
|
filename = file from which to read elastance matrix
|
||||||
*read_inv* value = filename
|
*read_inv* value = filename
|
||||||
filename = file from which to read inverted matrix
|
filename = file from which to read inverted matrix
|
||||||
|
*qtotal* value = number or *v_* equal-style variable
|
||||||
|
add overall potential so that all electrode charges add up to *qtotal*
|
||||||
|
*eta* value = d_propname
|
||||||
|
d_propname = a custom double vector defined via fix property/atom
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
@ -249,6 +253,24 @@ be enabled if any electrode particle has the same type as any
|
|||||||
electrolyte particle (which would be unusual in a typical simulation)
|
electrolyte particle (which would be unusual in a typical simulation)
|
||||||
and the fix will issue an error in that case.
|
and the fix will issue an error in that case.
|
||||||
|
|
||||||
|
.. versionchanged:: qtotal
|
||||||
|
|
||||||
|
The keyword *qtotal* causes *fix electrode/conp* and *fix electrode/thermo*
|
||||||
|
to add an overall potential to all electrodes so that the total charge on
|
||||||
|
the electrodes is a specified amount (which may be an equal-style variable).
|
||||||
|
For example, if a user wanted to simulate a solution of excess cations
|
||||||
|
such that the total electrolyte charge is +2, setting *qtotal -2* would cause
|
||||||
|
the total electrode charge to be -2, so that the simulation box remains overall
|
||||||
|
electroneutral. Since *fix electrode/conq* constrains the total charges of
|
||||||
|
individual electrodes, and since *symm on* constrains the total charge of all
|
||||||
|
electrodes to be zero, either option is incompatible with the *qtotal* keyword
|
||||||
|
(even if *qtotal* is set to zero).
|
||||||
|
|
||||||
|
The keyword *eta* takes the name of a custom double vector defined via fix
|
||||||
|
property/atom. The values will be used instead of the standard eta value. The
|
||||||
|
property/atom fix must be for vector of double values and use the *ghost on*
|
||||||
|
option.
|
||||||
|
|
||||||
Restart, fix_modify, output, run start/stop, minimize info
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
#!/usr/env/python3
|
#!/usr/env/python3
|
||||||
|
|
||||||
import sys
|
|
||||||
import os.path as op
|
import os.path as op
|
||||||
|
import sys
|
||||||
|
|
||||||
|
|
||||||
def rel_error(out, ref):
|
def rel_error(out, ref):
|
||||||
@ -49,5 +49,5 @@ for label, ref, out in out_lines:
|
|||||||
error = rel_error(out, ref)
|
error = rel_error(out, ref)
|
||||||
lines.append(f"{label}: {out:.5f}, {error:.5f}\n")
|
lines.append(f"{label}: {out:.5f}, {error:.5f}\n")
|
||||||
|
|
||||||
with open("madelung.txt", 'a') as f:
|
with open("madelung.txt", "a") as f:
|
||||||
f.writelines(lines)
|
f.writelines(lines)
|
||||||
|
|||||||
14
examples/PACKAGES/electrode/madelung/in.eta
Normal file
14
examples/PACKAGES/electrode/madelung/in.eta
Normal file
@ -0,0 +1,14 @@
|
|||||||
|
boundary p p f
|
||||||
|
kspace_style ewald/electrode 1.0e-8
|
||||||
|
kspace_modify slab 8.0 # ew3dc
|
||||||
|
|
||||||
|
include "settings.mod" # styles, computes, groups and fixes
|
||||||
|
|
||||||
|
thermo_style custom step pe c_qbot c_qtop
|
||||||
|
fix feta all property/atom d_eta ghost on
|
||||||
|
set group bot d_eta 2.0
|
||||||
|
set group top d_eta 2.0
|
||||||
|
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
14
examples/PACKAGES/electrode/madelung/in.eta_cg
Normal file
14
examples/PACKAGES/electrode/madelung/in.eta_cg
Normal file
@ -0,0 +1,14 @@
|
|||||||
|
boundary p p f
|
||||||
|
kspace_style ewald/electrode 1.0e-8
|
||||||
|
kspace_modify slab 8.0 # ew3dc
|
||||||
|
|
||||||
|
include "settings.mod" # styles, computes, groups and fixes
|
||||||
|
|
||||||
|
thermo_style custom step pe c_qbot c_qtop
|
||||||
|
fix feta all property/atom d_eta ghost on
|
||||||
|
set group bot d_eta 0.5
|
||||||
|
set group top d_eta 3.0
|
||||||
|
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
14
examples/PACKAGES/electrode/madelung/in.eta_mix
Normal file
14
examples/PACKAGES/electrode/madelung/in.eta_mix
Normal file
@ -0,0 +1,14 @@
|
|||||||
|
boundary p p f
|
||||||
|
kspace_style ewald/electrode 1.0e-8
|
||||||
|
kspace_modify slab 8.0 # ew3dc
|
||||||
|
|
||||||
|
include "settings.mod" # styles, computes, groups and fixes
|
||||||
|
|
||||||
|
thermo_style custom step pe c_qbot c_qtop
|
||||||
|
fix feta all property/atom d_eta ghost on
|
||||||
|
set group bot d_eta 0.5
|
||||||
|
set group top d_eta 3.0
|
||||||
|
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
138
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta.g++.1
Normal file
138
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta.g++.1
Normal file
@ -0,0 +1,138 @@
|
|||||||
|
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-668-g5b6c0c6b56)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
boundary p p f
|
||||||
|
kspace_style ewald/electrode 1.0e-8
|
||||||
|
kspace_modify slab 8.0 # ew3dc
|
||||||
|
|
||||||
|
include "settings.mod" # styles, computes, groups and fixes
|
||||||
|
# set boundary in main script because ffield is periodic
|
||||||
|
units real
|
||||||
|
# distribute electrode atoms among all processors:
|
||||||
|
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||||
|
|
||||||
|
atom_style full
|
||||||
|
pair_style lj/cut/coul/long 12
|
||||||
|
|
||||||
|
read_data "data.au-elyt"
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 -10) to (1 1 10)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
group bot type 1
|
||||||
|
1 atoms in group bot
|
||||||
|
group top type 2
|
||||||
|
1 atoms in group top
|
||||||
|
|
||||||
|
# get electrode charges
|
||||||
|
variable q atom q
|
||||||
|
compute qbot bot reduce sum v_q
|
||||||
|
compute qtop top reduce sum v_q
|
||||||
|
|
||||||
|
compute compute_pe all pe
|
||||||
|
variable vpe equal c_compute_pe
|
||||||
|
variable charge equal c_qtop
|
||||||
|
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
|
||||||
|
|
||||||
|
thermo_style custom step pe c_qbot c_qtop
|
||||||
|
fix feta all property/atom d_eta ghost on
|
||||||
|
set group bot d_eta 2.0
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
set group top d_eta 2.0
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
|
||||||
|
2 atoms in group conp_group
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- fix electrode command:
|
||||||
|
|
||||||
|
@article{Ahrens2022
|
||||||
|
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
|
||||||
|
doi = {10.1063/5.0099239},
|
||||||
|
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
|
||||||
|
journal = {The Journal of Chemical Physics},
|
||||||
|
year = {2022}
|
||||||
|
volume = {157},
|
||||||
|
pages = {084801},
|
||||||
|
}
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Ewald/electrode initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
|
||||||
|
G vector (1/distance) = 0.32261103
|
||||||
|
estimated absolute RMS force accuracy = 3.8272011e-06
|
||||||
|
estimated relative force accuracy = 1.1525502e-08
|
||||||
|
KSpace vectors: actual max1d max3d = 52 50 515150
|
||||||
|
kxmax kymax kzmax = 1 1 50
|
||||||
|
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, bins = 1 1 3
|
||||||
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||||
|
(1) pair lj/cut/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) fix electrode/conp, perpetual, copy from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:965)
|
||||||
|
139.943964815502, 0.279214485147238
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.2 | 144.2 Mbytes
|
||||||
|
Step PotEng c_qbot c_qtop
|
||||||
|
0 139.94396 -0.27921449 0.27921449
|
||||||
|
Loop time of 2.191e-06 on 1 procs for 0 steps with 4 atoms
|
||||||
|
|
||||||
|
91.3% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Kspace | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.191e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 4 ave 4 max 4 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 3596 ave 3596 max 3596 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 4790 ave 4790 max 4790 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 4790
|
||||||
|
Ave neighs/atom = 1197.5
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
139
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_cg.g++.1
Normal file
139
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_cg.g++.1
Normal file
@ -0,0 +1,139 @@
|
|||||||
|
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-668-g5b6c0c6b56)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
boundary p p f
|
||||||
|
kspace_style ewald/electrode 1.0e-8
|
||||||
|
kspace_modify slab 8.0 # ew3dc
|
||||||
|
|
||||||
|
include "settings.mod" # styles, computes, groups and fixes
|
||||||
|
# set boundary in main script because ffield is periodic
|
||||||
|
units real
|
||||||
|
# distribute electrode atoms among all processors:
|
||||||
|
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||||
|
|
||||||
|
atom_style full
|
||||||
|
pair_style lj/cut/coul/long 12
|
||||||
|
|
||||||
|
read_data "data.au-elyt"
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 -10) to (1 1 10)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
group bot type 1
|
||||||
|
1 atoms in group bot
|
||||||
|
group top type 2
|
||||||
|
1 atoms in group top
|
||||||
|
|
||||||
|
# get electrode charges
|
||||||
|
variable q atom q
|
||||||
|
compute qbot bot reduce sum v_q
|
||||||
|
compute qtop top reduce sum v_q
|
||||||
|
|
||||||
|
compute compute_pe all pe
|
||||||
|
variable vpe equal c_compute_pe
|
||||||
|
variable charge equal c_qtop
|
||||||
|
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
|
||||||
|
|
||||||
|
thermo_style custom step pe c_qbot c_qtop
|
||||||
|
fix feta all property/atom d_eta ghost on
|
||||||
|
set group bot d_eta 0.5
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
set group top d_eta 3.0
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6
|
||||||
|
2 atoms in group conp_group
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- fix electrode command:
|
||||||
|
|
||||||
|
@article{Ahrens2022
|
||||||
|
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
|
||||||
|
doi = {10.1063/5.0099239},
|
||||||
|
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
|
||||||
|
journal = {The Journal of Chemical Physics},
|
||||||
|
year = {2022}
|
||||||
|
volume = {157},
|
||||||
|
pages = {084801},
|
||||||
|
}
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Ewald/electrode initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
|
||||||
|
G vector (1/distance) = 0.32261103
|
||||||
|
estimated absolute RMS force accuracy = 3.8272011e-06
|
||||||
|
estimated relative force accuracy = 1.1525502e-08
|
||||||
|
KSpace vectors: actual max1d max3d = 52 50 515150
|
||||||
|
kxmax kymax kzmax = 1 1 50
|
||||||
|
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, bins = 1 1 3
|
||||||
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||||
|
(1) pair lj/cut/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) fix electrode/conp, perpetual, copy from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:965)
|
||||||
|
165.519373910316, 0.29521534552818
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.2 | 144.2 Mbytes
|
||||||
|
Step PotEng c_qbot c_qtop
|
||||||
|
0 165.51937 -0.29521535 0.29521535
|
||||||
|
Loop time of 2.797e-06 on 1 procs for 0 steps with 4 atoms
|
||||||
|
|
||||||
|
71.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Kspace | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.797e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 4 ave 4 max 4 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 3596 ave 3596 max 3596 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 4790 ave 4790 max 4790 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 4790
|
||||||
|
Ave neighs/atom = 1197.5
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Average conjugate gradient steps: 1
|
||||||
|
Total wall time: 0:00:00
|
||||||
138
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_mix.g++.1
Normal file
138
examples/PACKAGES/electrode/madelung/log.19Feb2024.eta_mix.g++.1
Normal file
@ -0,0 +1,138 @@
|
|||||||
|
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-668-g5b6c0c6b56)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
boundary p p f
|
||||||
|
kspace_style ewald/electrode 1.0e-8
|
||||||
|
kspace_modify slab 8.0 # ew3dc
|
||||||
|
|
||||||
|
include "settings.mod" # styles, computes, groups and fixes
|
||||||
|
# set boundary in main script because ffield is periodic
|
||||||
|
units real
|
||||||
|
# distribute electrode atoms among all processors:
|
||||||
|
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||||
|
|
||||||
|
atom_style full
|
||||||
|
pair_style lj/cut/coul/long 12
|
||||||
|
|
||||||
|
read_data "data.au-elyt"
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 -10) to (1 1 10)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
4 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
group bot type 1
|
||||||
|
1 atoms in group bot
|
||||||
|
group top type 2
|
||||||
|
1 atoms in group top
|
||||||
|
|
||||||
|
# get electrode charges
|
||||||
|
variable q atom q
|
||||||
|
compute qbot bot reduce sum v_q
|
||||||
|
compute qtop top reduce sum v_q
|
||||||
|
|
||||||
|
compute compute_pe all pe
|
||||||
|
variable vpe equal c_compute_pe
|
||||||
|
variable charge equal c_qtop
|
||||||
|
fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
|
||||||
|
|
||||||
|
thermo_style custom step pe c_qbot c_qtop
|
||||||
|
fix feta all property/atom d_eta ghost on
|
||||||
|
set group bot d_eta 0.5
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
set group top d_eta 3.0
|
||||||
|
Setting atom values ...
|
||||||
|
1 settings made for d_eta
|
||||||
|
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
|
||||||
|
2 atoms in group conp_group
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- fix electrode command:
|
||||||
|
|
||||||
|
@article{Ahrens2022
|
||||||
|
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
|
||||||
|
doi = {10.1063/5.0099239},
|
||||||
|
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
|
||||||
|
journal = {The Journal of Chemical Physics},
|
||||||
|
year = {2022}
|
||||||
|
volume = {157},
|
||||||
|
pages = {084801},
|
||||||
|
}
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||||
|
Ewald/electrode initialization ...
|
||||||
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||||
|
WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
|
||||||
|
G vector (1/distance) = 0.32261103
|
||||||
|
estimated absolute RMS force accuracy = 3.8272011e-06
|
||||||
|
estimated relative force accuracy = 1.1525502e-08
|
||||||
|
KSpace vectors: actual max1d max3d = 52 50 515150
|
||||||
|
kxmax kymax kzmax = 1 1 50
|
||||||
|
Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 14
|
||||||
|
ghost atom cutoff = 14
|
||||||
|
binsize = 7, bins = 1 1 3
|
||||||
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||||
|
(1) pair lj/cut/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) fix electrode/conp, perpetual, copy from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:965)
|
||||||
|
165.519373910316, 0.295215345528172
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.2 | 144.2 Mbytes
|
||||||
|
Step PotEng c_qbot c_qtop
|
||||||
|
0 165.51937 -0.29521535 0.29521535
|
||||||
|
Loop time of 2.18e-06 on 1 procs for 0 steps with 4 atoms
|
||||||
|
|
||||||
|
91.7% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Kspace | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.18e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 4 ave 4 max 4 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 3596 ave 3596 max 3596 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 4790 ave 4790 max 4790 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 4790
|
||||||
|
Ave neighs/atom = 1197.5
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -3,7 +3,6 @@
|
|||||||
import numpy as np
|
import numpy as np
|
||||||
from scipy.special import erf
|
from scipy.special import erf
|
||||||
|
|
||||||
ETA = 2
|
|
||||||
SQRT2 = np.sqrt(2)
|
SQRT2 = np.sqrt(2)
|
||||||
COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units
|
COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units
|
||||||
QE2F = 23.060549
|
QE2F = 23.060549
|
||||||
@ -17,14 +16,14 @@ def lattice(length):
|
|||||||
return np.array(np.meshgrid(x, y)).T.reshape(-1, 2)
|
return np.array(np.meshgrid(x, y)).T.reshape(-1, 2)
|
||||||
|
|
||||||
|
|
||||||
def a_element(r):
|
def a_element(r, eta):
|
||||||
"""Coulomb contribution of two Gaussians"""
|
"""Coulomb contribution of two Gaussians"""
|
||||||
return erf(ETA / SQRT2 * r) / r
|
return erf(eta * r) / r
|
||||||
|
|
||||||
|
|
||||||
def b_element(r, q):
|
def b_element(r, q, eta):
|
||||||
"""Coulomb contribution of a Gaussian with a point charge"""
|
"""Coulomb contribution of a Gaussian with a point charge"""
|
||||||
return q * erf(ETA * r) / r
|
return q * erf(eta * r) / r
|
||||||
|
|
||||||
|
|
||||||
a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2)
|
a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2)
|
||||||
@ -36,59 +35,65 @@ v = np.array([-0.5, 0.5]) * (QE2F / COULOMB)
|
|||||||
|
|
||||||
# distances to images within electrode and to opposite electrode
|
# distances to images within electrode and to opposite electrode
|
||||||
distances = a * np.linalg.norm(lattice(LENGTH), axis=1)
|
distances = a * np.linalg.norm(lattice(LENGTH), axis=1)
|
||||||
opposite_distances = np.sqrt(np.square(distances) + distance_plates ** 2)
|
opposite_distances = np.sqrt(np.square(distances) + distance_plates**2)
|
||||||
|
|
||||||
# self interaction and within original box
|
for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
|
||||||
A_11 = np.sqrt(2 / np.pi) * ETA
|
eta_mix = np.prod(eta_elec) / np.sqrt(np.sum(np.square(eta_elec)))
|
||||||
A_12 = erf(ETA * distance_plates / SQRT2) / distance_plates
|
# self interaction and within original box
|
||||||
|
A_11 = np.sqrt(2 / np.pi) * eta_elec[0]
|
||||||
|
A_22 = np.sqrt(2 / np.pi) * eta_elec[1]
|
||||||
|
A_12 = erf(eta_mix * distance_plates) / distance_plates
|
||||||
|
|
||||||
# interaction with periodic images
|
# interaction with periodic images
|
||||||
A_11 += 4 * np.sum(a_element(distances))
|
A_11 += 4 * np.sum(a_element(distances, eta_elec[0] / SQRT2))
|
||||||
A_12 += 4 * np.sum(a_element(opposite_distances))
|
A_22 += 4 * np.sum(a_element(distances, eta_elec[1] / SQRT2))
|
||||||
A = np.array([[A_11, A_12], [A_12, A_11]])
|
A_12 += 4 * np.sum(a_element(opposite_distances, eta_mix))
|
||||||
inv = np.linalg.inv(A)
|
A = np.array([[A_11, A_12], [A_12, A_22]])
|
||||||
e = np.array([1, 1])
|
inv = np.linalg.inv(A)
|
||||||
inv -= np.matmul(inv, np.matmul(np.outer(e, e), inv)) / np.dot(e, np.dot(inv, e))
|
e = np.array([1, 1])
|
||||||
|
inv -= np.matmul(inv, np.matmul(np.outer(e, e), inv)) / np.dot(e, np.dot(inv, e))
|
||||||
|
|
||||||
# electrode-electrolyte interaction
|
# electrode-electrolyte interaction
|
||||||
b = []
|
b = []
|
||||||
for x in x_elec:
|
for x, eta in zip(x_elec, eta_elec):
|
||||||
bi = 0
|
bi = 0
|
||||||
for y, q in zip(x_elyt, q_elyt):
|
for y, q in zip(x_elyt, q_elyt):
|
||||||
d = abs(y - x)
|
d = abs(y - x)
|
||||||
bi += b_element(d, q)
|
bi += b_element(d, q, eta)
|
||||||
image_distances = np.sqrt(np.square(distances) + d ** 2)
|
image_distances = np.sqrt(np.square(distances) + d**2)
|
||||||
bi += 4 * np.sum(b_element(image_distances, q))
|
bi += 4 * np.sum(b_element(image_distances, q, eta))
|
||||||
b.append(bi)
|
b.append(bi)
|
||||||
b = np.array(b)
|
b = np.array(b)
|
||||||
|
|
||||||
# electrolyte-electrolyte energy
|
# electrolyte-electrolyte energy
|
||||||
elyt_11 = 4 * np.sum(1 / distances)
|
elyt_11 = 4 * np.sum(1 / distances)
|
||||||
distance_elyt = x_elyt[1] - x_elyt[0]
|
distance_elyt = x_elyt[1] - x_elyt[0]
|
||||||
elyt_12 = 1 / distance_elyt + 4 * np.sum(
|
elyt_12 = 1 / distance_elyt + 4 * np.sum(
|
||||||
1 / np.sqrt(np.square(distances) + distance_elyt ** 2)
|
1 / np.sqrt(np.square(distances) + distance_elyt**2)
|
||||||
)
|
|
||||||
elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]])
|
|
||||||
energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt))
|
|
||||||
|
|
||||||
# electrode charges and energy
|
|
||||||
q = np.dot(inv, v - b)
|
|
||||||
energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt)
|
|
||||||
|
|
||||||
print(
|
|
||||||
"length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A"
|
|
||||||
)
|
|
||||||
print(
|
|
||||||
", ".join(
|
|
||||||
[
|
|
||||||
str(LENGTH),
|
|
||||||
f"{energy:.8f}",
|
|
||||||
f"{q[0]:.10f}",
|
|
||||||
f"{q[1]:.10f}",
|
|
||||||
f"{inv[0, 0]:.10f}",
|
|
||||||
f"{inv[0, 1]:.10f}",
|
|
||||||
f"{b[0]:.8f}",
|
|
||||||
f"{b[1]:.8f}",
|
|
||||||
]
|
|
||||||
)
|
)
|
||||||
)
|
elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]])
|
||||||
|
energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt))
|
||||||
|
|
||||||
|
# electrode charges and energy
|
||||||
|
q = np.dot(inv, v - b)
|
||||||
|
energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt)
|
||||||
|
|
||||||
|
with open(f"plate_cap{name}.csv", "w") as f:
|
||||||
|
f.write(
|
||||||
|
"length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A, b1 / e/A, b2 / e/A\n"
|
||||||
|
)
|
||||||
|
f.write(
|
||||||
|
", ".join(
|
||||||
|
[
|
||||||
|
str(LENGTH),
|
||||||
|
f"{energy:.8f}",
|
||||||
|
f"{q[0]:.10f}",
|
||||||
|
f"{q[1]:.10f}",
|
||||||
|
f"{inv[0, 0]:.10f}",
|
||||||
|
f"{inv[0, 1]:.10f}",
|
||||||
|
f"{b[0]:.8f}",
|
||||||
|
f"{b[1]:.8f}",
|
||||||
|
]
|
||||||
|
)
|
||||||
|
+ "\n"
|
||||||
|
)
|
||||||
|
|||||||
@ -7,17 +7,27 @@ if [ ! -f $lmpbin ]; then
|
|||||||
fi
|
fi
|
||||||
|
|
||||||
ref_out="plate_cap.csv"
|
ref_out="plate_cap.csv"
|
||||||
if [ ! -f $ref_out ]; then
|
ref_mix_out="plate_cap_eta_mix.csv"
|
||||||
|
if [ ! -f $ref_out ] || [ ! -f $ref_mix_out ]; then
|
||||||
echo "Generating reference data"
|
echo "Generating reference data"
|
||||||
python3 plate_cap.py > $ref_out
|
python3 plate_cap.py
|
||||||
fi
|
fi
|
||||||
|
|
||||||
echo "Running Lammps inputs"
|
echo "Running Lammps inputs"
|
||||||
|
# w/o eta mixing
|
||||||
rm -rf madelung.txt && touch madelung.txt
|
rm -rf madelung.txt && touch madelung.txt
|
||||||
for file in in.*; do
|
for file in in.eta in.ewald-ew3dc in.ewald-ew2d in.pppm-ew3dc in.cg; do
|
||||||
printf "\n$file\n" >> madelung.txt
|
printf "\n$file\n" >> madelung.txt
|
||||||
rm -f out.csv inv.csv vec.csv
|
rm -f out.csv inv.csv vec.csv
|
||||||
$lmpbin -i $file &> /dev/null
|
$lmpbin -i $file &> /dev/null
|
||||||
python3 eval.py $ref_out out.csv inv.csv vec.csv
|
python3 eval.py $ref_out out.csv inv.csv vec.csv
|
||||||
done
|
done
|
||||||
|
|
||||||
|
# with eta mixing
|
||||||
|
for file in in.eta_mix in.eta_cg; do
|
||||||
|
printf "\n$file\n" >> madelung.txt
|
||||||
|
rm -f out.csv inv.csv vec.csv
|
||||||
|
$lmpbin -i $file &> /dev/null
|
||||||
|
python3 eval.py $ref_mix_out out.csv inv.csv vec.csv
|
||||||
|
done
|
||||||
cat madelung.txt
|
cat madelung.txt
|
||||||
|
|||||||
17
src/ELECTRODE/README
Normal file
17
src/ELECTRODE/README
Normal file
@ -0,0 +1,17 @@
|
|||||||
|
This package provides the "fix electrode/*" commands which can be used in a
|
||||||
|
LAMMPS input script. These fixes implement the constant potential method, which
|
||||||
|
minimizes the energy of electrodes as a function of atom charges at given
|
||||||
|
electric potentials or electrode charges.
|
||||||
|
|
||||||
|
See the doc page for the fix electrode/conp command to get started. There are
|
||||||
|
example scripts for using this package in examples/PACKAGES/electrode.
|
||||||
|
|
||||||
|
This package uses an external library in lib/electrode which must be compiled
|
||||||
|
before making LAMMPS. For a CMake build, the location of the LAPACK library
|
||||||
|
should be linked automatically. Alternatively, the "USE_INTERNAL_LINALG" option
|
||||||
|
can be used to enable the bundled library. See the doc page on "Packages with
|
||||||
|
extra build options" for more information.
|
||||||
|
|
||||||
|
The primary people who created this package are Ludwig Ahrens-Iwers, Shern Tee
|
||||||
|
(s.tee@griffith.edu.au) and Robert Meißner (robert.meissner@tuhh.de). Contact
|
||||||
|
them directly if you have questions.
|
||||||
@ -18,22 +18,20 @@
|
|||||||
#ifndef LMP_ELECTRODE_MATH_H
|
#ifndef LMP_ELECTRODE_MATH_H
|
||||||
#define LMP_ELECTRODE_MATH_H
|
#define LMP_ELECTRODE_MATH_H
|
||||||
|
|
||||||
|
#include "ewald_const.h"
|
||||||
#include "math_const.h"
|
#include "math_const.h"
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
using namespace EwaldConst;
|
||||||
|
|
||||||
namespace ElectrodeMath {
|
namespace ElectrodeMath {
|
||||||
static constexpr double EWALD_P = 0.3275911;
|
|
||||||
static constexpr double A1 = 0.254829592;
|
|
||||||
static constexpr double A2 = -0.284496736;
|
|
||||||
static constexpr double A3 = 1.421413741;
|
|
||||||
static constexpr double A4 = -1.453152027;
|
|
||||||
static constexpr double A5 = 1.061405429;
|
|
||||||
static constexpr double ERFCMAX = 5.8; // erfc(ERFCMAX) < machine epsilon(double)
|
static constexpr double ERFCMAX = 5.8; // erfc(ERFCMAX) < machine epsilon(double)
|
||||||
|
|
||||||
static double safe_erfc(double x)
|
static double safe_erfc(double x)
|
||||||
{
|
{
|
||||||
if (x > ERFCMAX) return 0.;
|
if (x > ERFCMAX) return 0.0;
|
||||||
double expm2 = exp(-x * x);
|
double expm2 = exp(-x * x);
|
||||||
double t = 1.0 / (1.0 + EWALD_P * x);
|
double t = 1.0 / (1.0 + EWALD_P * x);
|
||||||
return t * (A1 + t * (A2 + t * (A3 + t * (A4 + t * A5)))) * expm2;
|
return t * (A1 + t * (A2 + t * (A3 + t * (A4 + t * A5)))) * expm2;
|
||||||
@ -42,14 +40,14 @@ namespace ElectrodeMath {
|
|||||||
static double safe_derfcr(double x, double &erfc)
|
static double safe_derfcr(double x, double &erfc)
|
||||||
{
|
{
|
||||||
if (x > ERFCMAX) {
|
if (x > ERFCMAX) {
|
||||||
erfc = 0.;
|
erfc = 0.0;
|
||||||
return 0.;
|
return 0.0;
|
||||||
}
|
}
|
||||||
double x2 = x * x;
|
double x2 = x * x;
|
||||||
double expm2 = exp(-x2);
|
double expm2 = exp(-x2);
|
||||||
double t = 1.0 / (1.0 + EWALD_P * x);
|
double t = 1.0 / (1.0 + EWALD_P * x);
|
||||||
erfc = t * (A1 + t * (A2 + t * (A3 + t * (A4 + t * A5)))) * expm2;
|
erfc = t * (A1 + t * (A2 + t * (A3 + t * (A4 + t * A5)))) * expm2;
|
||||||
return -erfc - 2 * expm2 * x / MathConst::MY_PIS;
|
return -erfc - 2.0 * expm2 * x / MathConst::MY_PIS;
|
||||||
}
|
}
|
||||||
} // namespace ElectrodeMath
|
} // namespace ElectrodeMath
|
||||||
|
|
||||||
|
|||||||
@ -43,6 +43,7 @@ ElectrodeMatrix::ElectrodeMatrix(LAMMPS *lmp, int electrode_group, double eta) :
|
|||||||
groupbit = group->bitmask[igroup];
|
groupbit = group->bitmask[igroup];
|
||||||
ngroup = group->count(igroup);
|
ngroup = group->count(igroup);
|
||||||
this->eta = eta;
|
this->eta = eta;
|
||||||
|
etaflag = false;
|
||||||
tfflag = false;
|
tfflag = false;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -72,6 +73,14 @@ void ElectrodeMatrix::setup_tf(const std::map<int, double> &tf_types)
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ElectrodeMatrix::setup_eta(int index)
|
||||||
|
{
|
||||||
|
etaflag = true;
|
||||||
|
eta_index = index;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void ElectrodeMatrix::compute_array(double **array, bool timer_flag)
|
void ElectrodeMatrix::compute_array(double **array, bool timer_flag)
|
||||||
{
|
{
|
||||||
// setting all entries of coulomb matrix to zero
|
// setting all entries of coulomb matrix to zero
|
||||||
@ -115,8 +124,6 @@ void ElectrodeMatrix::pair_contribution(double **array)
|
|||||||
int nlocal = atom->nlocal;
|
int nlocal = atom->nlocal;
|
||||||
int newton_pair = force->newton_pair;
|
int newton_pair = force->newton_pair;
|
||||||
|
|
||||||
double const etaij = eta * eta / sqrt(2.0 * eta * eta); // see mw ewald theory eq. (29)-(30)
|
|
||||||
|
|
||||||
// neighbor list will be ready because called from post_neighbor
|
// neighbor list will be ready because called from post_neighbor
|
||||||
inum = list->inum;
|
inum = list->inum;
|
||||||
ilist = list->ilist;
|
ilist = list->ilist;
|
||||||
@ -135,6 +142,7 @@ void ElectrodeMatrix::pair_contribution(double **array)
|
|||||||
xtmp = x[i][0];
|
xtmp = x[i][0];
|
||||||
ytmp = x[i][1];
|
ytmp = x[i][1];
|
||||||
ztmp = x[i][2];
|
ztmp = x[i][2];
|
||||||
|
double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta;
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
jlist = firstneigh[i];
|
jlist = firstneigh[i];
|
||||||
jnum = numneigh[i];
|
jnum = numneigh[i];
|
||||||
@ -152,6 +160,9 @@ void ElectrodeMatrix::pair_contribution(double **array)
|
|||||||
jtype = type[j];
|
jtype = type[j];
|
||||||
|
|
||||||
if (rsq < cutsq[itype][jtype]) {
|
if (rsq < cutsq[itype][jtype]) {
|
||||||
|
double const eta_j = etaflag ? atom->dvector[eta_index][j] : eta;
|
||||||
|
double const etaij = eta_i * eta_j / sqrt(eta_i * eta_i + eta_j * eta_j);
|
||||||
|
|
||||||
r = sqrt(rsq);
|
r = sqrt(rsq);
|
||||||
rinv = 1.0 / r;
|
rinv = 1.0 / r;
|
||||||
aij = rinv;
|
aij = rinv;
|
||||||
@ -178,7 +189,10 @@ void ElectrodeMatrix::self_contribution(double **array)
|
|||||||
const double preta = MY_SQRT2 / MY_PIS;
|
const double preta = MY_SQRT2 / MY_PIS;
|
||||||
|
|
||||||
for (int i = 0; i < nlocal; i++)
|
for (int i = 0; i < nlocal; i++)
|
||||||
if (mask[i] & groupbit) { array[mpos[i]][mpos[i]] += preta * eta - selfint; }
|
if (mask[i] & groupbit) {
|
||||||
|
double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta;
|
||||||
|
array[mpos[i]][mpos[i]] += preta * eta_i - selfint;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -30,6 +30,7 @@ class ElectrodeMatrix : protected Pointers {
|
|||||||
ElectrodeMatrix(class LAMMPS *, int, double);
|
ElectrodeMatrix(class LAMMPS *, int, double);
|
||||||
void setup(const std::unordered_map<tagint, int> &, class Pair *, class NeighList *);
|
void setup(const std::unordered_map<tagint, int> &, class Pair *, class NeighList *);
|
||||||
void setup_tf(const std::map<int, double> &);
|
void setup_tf(const std::map<int, double> &);
|
||||||
|
void setup_eta(int);
|
||||||
void compute_array(double **, bool);
|
void compute_array(double **, bool);
|
||||||
int igroup;
|
int igroup;
|
||||||
|
|
||||||
@ -39,6 +40,8 @@ class ElectrodeMatrix : protected Pointers {
|
|||||||
double **cutsq;
|
double **cutsq;
|
||||||
double g_ewald, eta;
|
double g_ewald, eta;
|
||||||
bool tfflag;
|
bool tfflag;
|
||||||
|
bool etaflag;
|
||||||
|
int eta_index;
|
||||||
std::map<int, double> tf_types;
|
std::map<int, double> tf_types;
|
||||||
std::unordered_map<tagint, int> tag_to_iele;
|
std::unordered_map<tagint, int> tag_to_iele;
|
||||||
bool assigned;
|
bool assigned;
|
||||||
|
|||||||
@ -29,6 +29,7 @@
|
|||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "pair.h"
|
#include "pair.h"
|
||||||
|
|
||||||
|
#include <cassert>
|
||||||
#include <cmath>
|
#include <cmath>
|
||||||
#include <exception>
|
#include <exception>
|
||||||
|
|
||||||
@ -47,6 +48,7 @@ ElectrodeVector::ElectrodeVector(LAMMPS *lmp, int sensor_group, int source_group
|
|||||||
source_grpbit = group->bitmask[source_group];
|
source_grpbit = group->bitmask[source_group];
|
||||||
this->eta = eta;
|
this->eta = eta;
|
||||||
tfflag = false;
|
tfflag = false;
|
||||||
|
etaflag = false;
|
||||||
|
|
||||||
kspace_time_total = 0;
|
kspace_time_total = 0;
|
||||||
pair_time_total = 0;
|
pair_time_total = 0;
|
||||||
@ -93,6 +95,14 @@ void ElectrodeVector::setup_tf(const std::map<int, double> &tf_types)
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ElectrodeVector::setup_eta(int index)
|
||||||
|
{
|
||||||
|
etaflag = true;
|
||||||
|
eta_index = index;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void ElectrodeVector::compute_vector(double *vector)
|
void ElectrodeVector::compute_vector(double *vector)
|
||||||
{
|
{
|
||||||
MPI_Barrier(world);
|
MPI_Barrier(world);
|
||||||
@ -121,7 +131,6 @@ void ElectrodeVector::compute_vector(double *vector)
|
|||||||
|
|
||||||
void ElectrodeVector::pair_contribution(double *vector)
|
void ElectrodeVector::pair_contribution(double *vector)
|
||||||
{
|
{
|
||||||
double const etaij = eta * MY_ISQRT2;
|
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
double *q = atom->q;
|
double *q = atom->q;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
@ -142,6 +151,7 @@ void ElectrodeVector::pair_contribution(double *vector)
|
|||||||
double const xtmp = x[i][0];
|
double const xtmp = x[i][0];
|
||||||
double const ytmp = x[i][1];
|
double const ytmp = x[i][1];
|
||||||
double const ztmp = x[i][2];
|
double const ztmp = x[i][2];
|
||||||
|
double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta;
|
||||||
int itype = type[i];
|
int itype = type[i];
|
||||||
int *jlist = firstneigh[i];
|
int *jlist = firstneigh[i];
|
||||||
int jnum = numneigh[i];
|
int jnum = numneigh[i];
|
||||||
@ -158,18 +168,22 @@ void ElectrodeVector::pair_contribution(double *vector)
|
|||||||
double const rsq = delx * delx + dely * dely + delz * delz;
|
double const rsq = delx * delx + dely * dely + delz * delz;
|
||||||
int jtype = type[j];
|
int jtype = type[j];
|
||||||
if (rsq >= cutsq[itype][jtype]) continue;
|
if (rsq >= cutsq[itype][jtype]) continue;
|
||||||
|
double const eta_j = etaflag ? atom->dvector[eta_index][j] : eta;
|
||||||
|
double etaij;
|
||||||
|
if (i_in_sensor && j_in_sensor) {
|
||||||
|
etaij = eta_i * eta_j / sqrt(eta_i * eta_i + eta_j * eta_j);
|
||||||
|
} else if (i_in_sensor) {
|
||||||
|
etaij = eta_i;
|
||||||
|
} else {
|
||||||
|
assert(j_in_sensor);
|
||||||
|
etaij = eta_j;
|
||||||
|
}
|
||||||
double const r = sqrt(rsq);
|
double const r = sqrt(rsq);
|
||||||
double const rinv = 1.0 / r;
|
double const rinv = 1.0 / r;
|
||||||
double aij = rinv;
|
double aij = rinv;
|
||||||
aij *= ElectrodeMath::safe_erfc(g_ewald * r);
|
aij *= ElectrodeMath::safe_erfc(g_ewald * r);
|
||||||
if (invert_source)
|
aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv;
|
||||||
aij -= ElectrodeMath::safe_erfc(eta * r) * rinv;
|
if (i_in_sensor) { vector[i] += aij * q[j]; }
|
||||||
else
|
|
||||||
aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv;
|
|
||||||
if (i_in_sensor) {
|
|
||||||
vector[i] += aij * q[j];
|
|
||||||
//} else if (j_in_sensor) {
|
|
||||||
}
|
|
||||||
if (j_in_sensor && (!invert_source || !i_in_sensor)) { vector[j] += aij * q[i]; }
|
if (j_in_sensor && (!invert_source || !i_in_sensor)) { vector[j] += aij * q[i]; }
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -189,9 +203,10 @@ void ElectrodeVector::self_contribution(double *vector)
|
|||||||
|
|
||||||
for (int ii = 0; ii < inum; ii++) {
|
for (int ii = 0; ii < inum; ii++) {
|
||||||
int const i = ilist[ii];
|
int const i = ilist[ii];
|
||||||
|
double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta;
|
||||||
bool const i_in_sensor = (mask[i] & groupbit);
|
bool const i_in_sensor = (mask[i] & groupbit);
|
||||||
bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source;
|
bool const i_in_source = !!(mask[i] & source_grpbit) != invert_source;
|
||||||
if (i_in_sensor && i_in_source) vector[i] += (preta * eta - selfint) * q[i];
|
if (i_in_sensor && i_in_source) vector[i] += (preta * eta_i - selfint) * q[i];
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -29,6 +29,7 @@ class ElectrodeVector : protected Pointers {
|
|||||||
~ElectrodeVector() override;
|
~ElectrodeVector() override;
|
||||||
void setup(class Pair *, class NeighList *, bool);
|
void setup(class Pair *, class NeighList *, bool);
|
||||||
void setup_tf(const std::map<int, double> &);
|
void setup_tf(const std::map<int, double> &);
|
||||||
|
void setup_eta(int);
|
||||||
void compute_vector(double *);
|
void compute_vector(double *);
|
||||||
int igroup, source_group;
|
int igroup, source_group;
|
||||||
|
|
||||||
@ -39,6 +40,8 @@ class ElectrodeVector : protected Pointers {
|
|||||||
double **cutsq;
|
double **cutsq;
|
||||||
double g_ewald, eta;
|
double g_ewald, eta;
|
||||||
bool tfflag;
|
bool tfflag;
|
||||||
|
bool etaflag;
|
||||||
|
int eta_index;
|
||||||
std::map<int, double> tf_types;
|
std::map<int, double> tf_types;
|
||||||
class Pair *pair;
|
class Pair *pair;
|
||||||
class NeighList *list;
|
class NeighList *list;
|
||||||
|
|||||||
@ -98,26 +98,30 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
top_group = 0;
|
top_group = 0;
|
||||||
intelflag = false;
|
intelflag = false;
|
||||||
tfflag = false;
|
tfflag = false;
|
||||||
|
etaflag = false;
|
||||||
timer_flag = false;
|
timer_flag = false;
|
||||||
|
|
||||||
update_time = 0;
|
update_time = 0;
|
||||||
mult_time = 0;
|
mult_time = 0;
|
||||||
n_call = n_cg_step = 0;
|
n_call = n_cg_step = 0;
|
||||||
|
|
||||||
|
qtotal = 0.;
|
||||||
|
qtotal_var_style = VarStyle::UNSET;
|
||||||
|
|
||||||
// read fix command
|
// read fix command
|
||||||
fixname = std::string(arg[0]);
|
fixname = std::string(arg[0]);
|
||||||
groups = std::vector<int>(1, igroup);
|
groups = std::vector<int>(1, igroup);
|
||||||
group_bits = std::vector<int>(1, groupbit);
|
group_bits = std::vector<int>(1, groupbit);
|
||||||
group_psi_var_names = std::vector<std::string>(1);
|
group_psi_var_names = std::vector<std::string>(1);
|
||||||
group_psi_var_styles = std::vector<VarStyle>(1, VarStyle::CONST);
|
group_psi_var_styles = std::vector<VarStyle>(1, VarStyle::CONST);
|
||||||
group_psi = std::vector<double>(1);
|
group_psi_const = std::vector<double>(1);
|
||||||
etypes_neighlists = false;
|
etypes_neighlists = false;
|
||||||
if (strstr(arg[3], "v_") == arg[3]) {
|
if (strstr(arg[3], "v_") == arg[3]) {
|
||||||
std::string vname = arg[3];
|
std::string vname = arg[3];
|
||||||
group_psi_var_names[0] = vname.substr(2);
|
group_psi_var_names[0] = vname.substr(2);
|
||||||
group_psi_var_styles[0] = VarStyle::EQUAL;
|
group_psi_var_styles[0] = VarStyle::EQUAL;
|
||||||
} else
|
} else
|
||||||
group_psi[0] = utils::numeric(FLERR, arg[3], false, lmp);
|
group_psi_const[0] = utils::numeric(FLERR, arg[3], false, lmp);
|
||||||
char *eta_str = arg[4];
|
char *eta_str = arg[4];
|
||||||
eta = utils::numeric(FLERR, eta_str, false, lmp);
|
eta = utils::numeric(FLERR, eta_str, false, lmp);
|
||||||
int iarg = 5;
|
int iarg = 5;
|
||||||
@ -133,12 +137,12 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
std::string vname = arg[iarg];
|
std::string vname = arg[iarg];
|
||||||
group_psi_var_names.push_back(vname.substr(2));
|
group_psi_var_names.push_back(vname.substr(2));
|
||||||
group_psi_var_styles.push_back(VarStyle::EQUAL);
|
group_psi_var_styles.push_back(VarStyle::EQUAL);
|
||||||
group_psi.push_back(0.);
|
group_psi_const.push_back(0.);
|
||||||
} else {
|
} else {
|
||||||
std::string null;
|
std::string null;
|
||||||
group_psi_var_names.push_back(null);
|
group_psi_var_names.push_back(null);
|
||||||
group_psi_var_styles.push_back(VarStyle::CONST);
|
group_psi_var_styles.push_back(VarStyle::CONST);
|
||||||
group_psi.push_back(utils::numeric(FLERR, arg[iarg], false, lmp));
|
group_psi_const.push_back(utils::numeric(FLERR, arg[iarg], false, lmp));
|
||||||
}
|
}
|
||||||
} else if ((strcmp(arg[iarg], "algo") == 0)) {
|
} else if ((strcmp(arg[iarg], "algo") == 0)) {
|
||||||
if (!default_algo) error->one(FLERR, "Algorithm can be set only once");
|
if (!default_algo) error->one(FLERR, "Algorithm can be set only once");
|
||||||
@ -196,8 +200,32 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
thermo_temp = force->boltz / force->qe2f * utils::numeric(FLERR, arg[++iarg], false, lmp);
|
thermo_temp = force->boltz / force->qe2f * utils::numeric(FLERR, arg[++iarg], false, lmp);
|
||||||
thermo_time = utils::numeric(FLERR, arg[++iarg], false, lmp);
|
thermo_time = utils::numeric(FLERR, arg[++iarg], false, lmp);
|
||||||
thermo_init = utils::inumeric(FLERR, arg[++iarg], false, lmp);
|
thermo_init = utils::inumeric(FLERR, arg[++iarg], false, lmp);
|
||||||
// toggle parameters
|
} else if ((strcmp(arg[iarg], "qtotal") == 0)) {
|
||||||
} else if ((strcmp(arg[iarg], "etypes") == 0)) {
|
if (iarg + 2 > narg) error->all(FLERR, "Need one argument after qtotal keyword");
|
||||||
|
if (strcmp(this->style, "electrode/conq") == 0)
|
||||||
|
error->all(FLERR, "qtotal keyword not available for electrode/conq");
|
||||||
|
++iarg;
|
||||||
|
if (strstr(arg[iarg], "v_") == arg[iarg]) {
|
||||||
|
std::string vname = arg[iarg];
|
||||||
|
qtotal_var_name = vname.substr(2);
|
||||||
|
qtotal_var_style = VarStyle::EQUAL;
|
||||||
|
} else {
|
||||||
|
qtotal = utils::numeric(FLERR, arg[iarg], false, lmp);
|
||||||
|
qtotal_var_style = VarStyle::CONST;
|
||||||
|
}
|
||||||
|
} else if ((strcmp(arg[iarg], "eta") == 0)) {
|
||||||
|
if (iarg + 2 > narg) error->all(FLERR, "Need two arguments after eta command");
|
||||||
|
etaflag = true;
|
||||||
|
int is_double, cols, ghost;
|
||||||
|
eta_index = atom->find_custom_ghost(arg[++iarg] + 2, is_double, cols, ghost);
|
||||||
|
if (eta_index == -1)
|
||||||
|
error->all(FLERR, "eta keyword requires name of previously defined property");
|
||||||
|
if (!is_double) error->all(FLERR, "eta keyword requires double-valued property/atom vector");
|
||||||
|
if (cols != 0) error->all(FLERR, "eta keyword requires property/atom vector not an array");
|
||||||
|
if (!ghost) error->all(FLERR, "eta keyword requires property/atom fix with ghost on");
|
||||||
|
}
|
||||||
|
// toggle parameters
|
||||||
|
else if ((strcmp(arg[iarg], "etypes") == 0)) {
|
||||||
etypes_neighlists = utils::logical(FLERR, arg[++iarg], false, lmp);
|
etypes_neighlists = utils::logical(FLERR, arg[++iarg], false, lmp);
|
||||||
} else if ((strncmp(arg[iarg], "symm", 4) == 0)) {
|
} else if ((strncmp(arg[iarg], "symm", 4) == 0)) {
|
||||||
symm = utils::logical(FLERR, arg[++iarg], false, lmp);
|
symm = utils::logical(FLERR, arg[++iarg], false, lmp);
|
||||||
@ -209,6 +237,12 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
iarg++;
|
iarg++;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (qtotal_var_style != VarStyle::UNSET) {
|
||||||
|
if (symm) error->all(FLERR, "{} cannot use qtotal keyword with symm on", this->style);
|
||||||
|
}
|
||||||
|
|
||||||
|
// computatonal potential
|
||||||
|
group_psi = std::vector<double>(groups.size());
|
||||||
// union of all coupled groups
|
// union of all coupled groups
|
||||||
std::string union_group = "conp_group";
|
std::string union_group = "conp_group";
|
||||||
std::string group_cmd = union_group + " union";
|
std::string group_cmd = union_group + " union";
|
||||||
@ -226,6 +260,7 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
if (need_elec_vector) elec_vector = new ElectrodeVector(lmp, igroup, igroup, eta, false);
|
if (need_elec_vector) elec_vector = new ElectrodeVector(lmp, igroup, igroup, eta, false);
|
||||||
assert(groups.size() == group_bits.size());
|
assert(groups.size() == group_bits.size());
|
||||||
assert(groups.size() == group_psi.size());
|
assert(groups.size() == group_psi.size());
|
||||||
|
assert(groups.size() == group_psi_const.size());
|
||||||
assert(groups.size() == group_psi_var_styles.size());
|
assert(groups.size() == group_psi_var_styles.size());
|
||||||
assert(groups.size() == group_psi_var_names.size());
|
assert(groups.size() == group_psi_var_names.size());
|
||||||
assert(igroup == elyt_vector->igroup);
|
assert(igroup == elyt_vector->igroup);
|
||||||
@ -375,6 +410,31 @@ void FixElectrodeConp::init()
|
|||||||
if (strncmp(modify->fix[i]->style, "electrode", 9) == 0) count++;
|
if (strncmp(modify->fix[i]->style, "electrode", 9) == 0) count++;
|
||||||
if (count > 1) error->all(FLERR, "More than one fix electrode");
|
if (count > 1) error->all(FLERR, "More than one fix electrode");
|
||||||
|
|
||||||
|
// make sure electrode atoms are not integrated if a matrix is used for electrode-electrode interaction
|
||||||
|
int const nlocal = atom->nlocal;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
Fix **fix = modify->fix;
|
||||||
|
if (matrix_algo) {
|
||||||
|
std::vector<char *> integrate_ids = std::vector<char *>();
|
||||||
|
for (int i = 0; i < modify->nfix; i++) {
|
||||||
|
if (fix[i]->time_integrate == 0) continue;
|
||||||
|
int electrode_mover = 0;
|
||||||
|
int fix_groupbit = fix[i]->groupbit;
|
||||||
|
for (int j = 0; j < nlocal; j++)
|
||||||
|
if ((mask[j] & fix_groupbit) && (mask[j] & groupbit)) electrode_mover = 1;
|
||||||
|
MPI_Allreduce(MPI_IN_PLACE, &electrode_mover, 1, MPI_INT, MPI_SUM, world);
|
||||||
|
if (electrode_mover && comm->me == 0) integrate_ids.push_back(fix[i]->id);
|
||||||
|
}
|
||||||
|
if (comm->me == 0)
|
||||||
|
for (char *fix_id : integrate_ids)
|
||||||
|
error->warning(
|
||||||
|
FLERR,
|
||||||
|
"Electrode atoms are integrated by fix {}, but fix electrode is using a matrix method. "
|
||||||
|
"For "
|
||||||
|
"mobile electrodes use the conjugate gradient algorithm without matrix ('algo cg').",
|
||||||
|
fix_id);
|
||||||
|
}
|
||||||
|
|
||||||
// check for package intel
|
// check for package intel
|
||||||
if (etypes_neighlists)
|
if (etypes_neighlists)
|
||||||
request_etypes_neighlists();
|
request_etypes_neighlists();
|
||||||
@ -449,6 +509,7 @@ void FixElectrodeConp::setup_post_neighbor()
|
|||||||
// get equal-style variable ids:
|
// get equal-style variable ids:
|
||||||
group_psi_var_ids = std::vector<int>(num_of_groups, -1);
|
group_psi_var_ids = std::vector<int>(num_of_groups, -1);
|
||||||
for (int g = 0; g < num_of_groups; g++) {
|
for (int g = 0; g < num_of_groups; g++) {
|
||||||
|
assert(group_psi_var_styles[g] != VarStyle::UNSET);
|
||||||
if (group_psi_var_styles[g] == VarStyle::CONST) continue;
|
if (group_psi_var_styles[g] == VarStyle::CONST) continue;
|
||||||
const char *var_name = group_psi_var_names[g].c_str();
|
const char *var_name = group_psi_var_names[g].c_str();
|
||||||
int var_id = input->variable->find(var_name);
|
int var_id = input->variable->find(var_name);
|
||||||
@ -457,13 +518,23 @@ void FixElectrodeConp::setup_post_neighbor()
|
|||||||
error->all(FLERR, "Variable '{}' for fix {} is not equal-style", var_name, style);
|
error->all(FLERR, "Variable '{}' for fix {} is not equal-style", var_name, style);
|
||||||
group_psi_var_ids[g] = var_id;
|
group_psi_var_ids[g] = var_id;
|
||||||
}
|
}
|
||||||
|
if (qtotal_var_style == VarStyle::EQUAL) {
|
||||||
|
const char *var_name = qtotal_var_name.c_str();
|
||||||
|
int var_id = input->variable->find(var_name);
|
||||||
|
if (var_id < 0) error->all(FLERR, "Variable '{}' for fix electrode does not exist", var_name);
|
||||||
|
if (!input->variable->equalstyle(var_id))
|
||||||
|
error->all(FLERR, "Variable '{}' for fix electrode is not equal-style", var_name);
|
||||||
|
qtotal_var_id = var_id;
|
||||||
|
}
|
||||||
|
|
||||||
// pair and list setups:
|
// pair and list setups:
|
||||||
|
|
||||||
evscale = force->qe2f / force->qqrd2e;
|
evscale = force->qe2f / force->qqrd2e;
|
||||||
elyt_vector->setup(pair, vec_neighlist, timer_flag);
|
elyt_vector->setup(pair, vec_neighlist, timer_flag);
|
||||||
|
if (etaflag) elyt_vector->setup_eta(eta_index);
|
||||||
if (need_elec_vector) {
|
if (need_elec_vector) {
|
||||||
elec_vector->setup(pair, mat_neighlist, timer_flag);
|
elec_vector->setup(pair, mat_neighlist, timer_flag);
|
||||||
|
if (etaflag) elec_vector->setup_eta(eta_index);
|
||||||
if (tfflag) elec_vector->setup_tf(tf_types);
|
if (tfflag) elec_vector->setup_tf(tf_types);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -498,7 +569,8 @@ void FixElectrodeConp::setup_post_neighbor()
|
|||||||
if (etypes_neighlists) neighbor->build_one(mat_neighlist, 0);
|
if (etypes_neighlists) neighbor->build_one(mat_neighlist, 0);
|
||||||
auto array_compute = std::unique_ptr<ElectrodeMatrix>(new ElectrodeMatrix(lmp, igroup, eta));
|
auto array_compute = std::unique_ptr<ElectrodeMatrix>(new ElectrodeMatrix(lmp, igroup, eta));
|
||||||
array_compute->setup(tag_to_iele, pair, mat_neighlist);
|
array_compute->setup(tag_to_iele, pair, mat_neighlist);
|
||||||
if (tfflag) { array_compute->setup_tf(tf_types); }
|
if (etaflag) array_compute->setup_eta(eta_index);
|
||||||
|
if (tfflag) array_compute->setup_tf(tf_types);
|
||||||
array_compute->compute_array(elastance, timer_flag);
|
array_compute->compute_array(elastance, timer_flag);
|
||||||
} // write_mat before proceeding
|
} // write_mat before proceeding
|
||||||
if (comm->me == 0 && write_mat) {
|
if (comm->me == 0 && write_mat) {
|
||||||
@ -805,6 +877,8 @@ void FixElectrodeConp::update_charges()
|
|||||||
}
|
}
|
||||||
MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world);
|
MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world);
|
||||||
update_psi(); // use for equal-style and conq
|
update_psi(); // use for equal-style and conq
|
||||||
|
if (qtotal_var_style != VarStyle::UNSET)
|
||||||
|
update_psi_qtotal(); // use for qtotal; same for thermo
|
||||||
for (int g = 0; g < num_of_groups; g++)
|
for (int g = 0; g < num_of_groups; g++)
|
||||||
for (int j = 0; j < nlocalele; j++) q_local[j] += sd_vectors[g][list_iele[j]] * group_psi[g];
|
for (int j = 0; j < nlocalele; j++) q_local[j] += sd_vectors[g][list_iele[j]] * group_psi[g];
|
||||||
MPI_Barrier(world);
|
MPI_Barrier(world);
|
||||||
@ -907,12 +981,22 @@ std::vector<double> FixElectrodeConp::gather_ngroup(std::vector<double> x_local)
|
|||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
ensure total electrode charge is 0 if symm
|
ensure total electrode charge is 0 if symm and qtotal if qtotal is used
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
std::vector<double> FixElectrodeConp::constraint_correction(std::vector<double> x)
|
std::vector<double> FixElectrodeConp::constraint_correction(std::vector<double> x)
|
||||||
{
|
{
|
||||||
return constraint_projection(std::move(x));
|
if (symm || qtotal_var_style != VarStyle::UNSET) {
|
||||||
|
if (qtotal_var_style == VarStyle::EQUAL) qtotal = input->variable->compute_equal(qtotal_var_id);
|
||||||
|
double sum = 0.;
|
||||||
|
for (double xi : x) sum += xi;
|
||||||
|
MPI_Allreduce(MPI_IN_PLACE, &sum, 1, MPI_DOUBLE, MPI_SUM, world);
|
||||||
|
if (qtotal_var_style != VarStyle::UNSET) sum -= qtotal;
|
||||||
|
sum /= ngroup;
|
||||||
|
for (double &xi : x) xi -= sum;
|
||||||
|
return x;
|
||||||
|
}
|
||||||
|
return x;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -921,7 +1005,7 @@ std::vector<double> FixElectrodeConp::constraint_correction(std::vector<double>
|
|||||||
|
|
||||||
std::vector<double> FixElectrodeConp::constraint_projection(std::vector<double> x)
|
std::vector<double> FixElectrodeConp::constraint_projection(std::vector<double> x)
|
||||||
{
|
{
|
||||||
if (symm) {
|
if (symm || qtotal_var_style != VarStyle::UNSET) {
|
||||||
double sum = 0.;
|
double sum = 0.;
|
||||||
for (double xi : x) sum += xi;
|
for (double xi : x) sum += xi;
|
||||||
MPI_Allreduce(MPI_IN_PLACE, &sum, 1, MPI_DOUBLE, MPI_SUM, world);
|
MPI_Allreduce(MPI_IN_PLACE, &sum, 1, MPI_DOUBLE, MPI_SUM, world);
|
||||||
@ -979,13 +1063,28 @@ std::vector<double> FixElectrodeConp::times_elastance(std::vector<double> x)
|
|||||||
void FixElectrodeConp::update_psi()
|
void FixElectrodeConp::update_psi()
|
||||||
{
|
{
|
||||||
for (int g = 0; g < num_of_groups; g++) {
|
for (int g = 0; g < num_of_groups; g++) {
|
||||||
if (group_psi_var_styles[g] == VarStyle::CONST) continue;
|
if (group_psi_var_styles[g] == VarStyle::CONST)
|
||||||
group_psi[g] = input->variable->compute_equal(group_psi_var_ids[g]);
|
group_psi[g] = group_psi_const[g];
|
||||||
|
else
|
||||||
|
group_psi[g] = input->variable->compute_equal(group_psi_var_ids[g]);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixElectrodeConp::update_psi_qtotal()
|
||||||
|
{
|
||||||
|
if (qtotal_var_style == VarStyle::EQUAL) qtotal = input->variable->compute_equal(qtotal_var_id);
|
||||||
|
double q_current = 0.;
|
||||||
|
for (int i = 0; i < num_of_groups; i++) {
|
||||||
|
q_current += sb_charges[i];
|
||||||
|
for (int j = 0; j < num_of_groups; j++) q_current += macro_capacitance[i][j] * group_psi[j];
|
||||||
|
}
|
||||||
|
double add_psi = (qtotal - q_current) / macro_capacitance_sum;
|
||||||
|
for (int i = 0; i < num_of_groups; i++) group_psi[i] += add_psi;
|
||||||
|
}
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void FixElectrodeConp::compute_macro_matrices()
|
void FixElectrodeConp::compute_macro_matrices()
|
||||||
{
|
{
|
||||||
assert(algo == Algo::MATRIX_INV);
|
assert(algo == Algo::MATRIX_INV);
|
||||||
@ -1041,6 +1140,10 @@ void FixElectrodeConp::compute_macro_matrices()
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
macro_capacitance_sum = 0.;
|
||||||
|
for (int i = 0; i < num_of_groups; i++)
|
||||||
|
for (int j = 0; j < num_of_groups; j++) macro_capacitance_sum += macro_capacitance[i][j];
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -1097,7 +1200,7 @@ double FixElectrodeConp::self_energy(int eflag)
|
|||||||
// corrections to energy due to self interaction
|
// corrections to energy due to self interaction
|
||||||
double const qqrd2e = force->qqrd2e;
|
double const qqrd2e = force->qqrd2e;
|
||||||
int const nlocal = atom->nlocal;
|
int const nlocal = atom->nlocal;
|
||||||
double const pre = eta / sqrt(MY_2PI) * qqrd2e;
|
double const pre = 1. / sqrt(MY_2PI) * qqrd2e;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
double *q = atom->q;
|
double *q = atom->q;
|
||||||
@ -1105,7 +1208,8 @@ double FixElectrodeConp::self_energy(int eflag)
|
|||||||
for (int i = 0; i < nlocal; i++) {
|
for (int i = 0; i < nlocal; i++) {
|
||||||
if (groupbit & mask[i]) {
|
if (groupbit & mask[i]) {
|
||||||
double const q2 = q[i] * q[i];
|
double const q2 = q[i] * q[i];
|
||||||
double e = pre * q2;
|
double ieta = etaflag ? atom->dvector[eta_index][i] : eta;
|
||||||
|
double e = ieta * pre * q2;
|
||||||
if (tfflag && (groupbit & mask[i])) e += 0.5 * qqrd2e * q2 * tf_types[type[i]];
|
if (tfflag && (groupbit & mask[i])) e += 0.5 * qqrd2e * q2 * tf_types[type[i]];
|
||||||
energy += e;
|
energy += e;
|
||||||
if (eflag) {
|
if (eflag) {
|
||||||
@ -1145,6 +1249,7 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag)
|
|||||||
double xtmp = x[i][0];
|
double xtmp = x[i][0];
|
||||||
double ytmp = x[i][1];
|
double ytmp = x[i][1];
|
||||||
double ztmp = x[i][2];
|
double ztmp = x[i][2];
|
||||||
|
double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta;
|
||||||
int itype = type[i];
|
int itype = type[i];
|
||||||
int *jlist = firstneigh[i];
|
int *jlist = firstneigh[i];
|
||||||
int jnum = numneigh[i];
|
int jnum = numneigh[i];
|
||||||
@ -1153,7 +1258,6 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag)
|
|||||||
int const j = jlist[jj] & NEIGHMASK;
|
int const j = jlist[jj] & NEIGHMASK;
|
||||||
bool j_in_ele = groupbit & mask[j];
|
bool j_in_ele = groupbit & mask[j];
|
||||||
if (!(i_in_ele || j_in_ele)) continue;
|
if (!(i_in_ele || j_in_ele)) continue;
|
||||||
double eta_ij = (i_in_ele && j_in_ele) ? eta / MY_SQRT2 : eta;
|
|
||||||
|
|
||||||
double delx = xtmp - x[j][0];
|
double delx = xtmp - x[j][0];
|
||||||
double dely = ytmp - x[j][1];
|
double dely = ytmp - x[j][1];
|
||||||
@ -1162,6 +1266,16 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag)
|
|||||||
int jtype = type[j];
|
int jtype = type[j];
|
||||||
|
|
||||||
if (rsq < force->pair->cutsq[itype][jtype]) {
|
if (rsq < force->pair->cutsq[itype][jtype]) {
|
||||||
|
double const eta_j = etaflag ? atom->dvector[eta_index][j] : eta;
|
||||||
|
double eta_ij;
|
||||||
|
if (i_in_ele && j_in_ele)
|
||||||
|
eta_ij = eta_i * eta_j / sqrt(eta_i * eta_i + eta_j * eta_j);
|
||||||
|
else if (i_in_ele)
|
||||||
|
eta_ij = eta_i;
|
||||||
|
else {
|
||||||
|
assert(j_in_ele);
|
||||||
|
eta_ij = eta_j;
|
||||||
|
}
|
||||||
double r2inv = 1.0 / rsq;
|
double r2inv = 1.0 / rsq;
|
||||||
double r = sqrt(rsq);
|
double r = sqrt(rsq);
|
||||||
double erfc_etar = 0.;
|
double erfc_etar = 0.;
|
||||||
|
|||||||
@ -70,7 +70,7 @@ class FixElectrodeConp : public Fix {
|
|||||||
|
|
||||||
protected:
|
protected:
|
||||||
enum class Algo { MATRIX_INV, MATRIX_CG, CG };
|
enum class Algo { MATRIX_INV, MATRIX_CG, CG };
|
||||||
enum class VarStyle { CONST, EQUAL };
|
enum class VarStyle { CONST, EQUAL, UNSET };
|
||||||
virtual void update_psi();
|
virtual void update_psi();
|
||||||
virtual void pre_update(){};
|
virtual void pre_update(){};
|
||||||
virtual void recompute_potential(std::vector<double>, std::vector<double>){};
|
virtual void recompute_potential(std::vector<double>, std::vector<double>){};
|
||||||
@ -79,6 +79,7 @@ class FixElectrodeConp : public Fix {
|
|||||||
virtual void compute_macro_matrices();
|
virtual void compute_macro_matrices();
|
||||||
std::vector<double> ele_ele_interaction(const std::vector<double> &);
|
std::vector<double> ele_ele_interaction(const std::vector<double> &);
|
||||||
std::vector<double> group_psi;
|
std::vector<double> group_psi;
|
||||||
|
std::vector<double> group_psi_const; // needed to undo qtotal psi updates
|
||||||
std::vector<int> group_bits;
|
std::vector<int> group_bits;
|
||||||
std::vector<int> groups;
|
std::vector<int> groups;
|
||||||
int num_of_groups;
|
int num_of_groups;
|
||||||
@ -100,6 +101,10 @@ class FixElectrodeConp : public Fix {
|
|||||||
std::string fixname; // used by electrode/ffield to set up internal efield
|
std::string fixname; // used by electrode/ffield to set up internal efield
|
||||||
bool intelflag;
|
bool intelflag;
|
||||||
inline virtual void intel_pack_buffers() {}
|
inline virtual void intel_pack_buffers() {}
|
||||||
|
double qtotal;
|
||||||
|
std::string qtotal_var_name;
|
||||||
|
int qtotal_var_id;
|
||||||
|
VarStyle qtotal_var_style;
|
||||||
|
|
||||||
private:
|
private:
|
||||||
std::string output_file_inv, output_file_mat, output_file_vec;
|
std::string output_file_inv, output_file_mat, output_file_vec;
|
||||||
@ -132,6 +137,8 @@ class FixElectrodeConp : public Fix {
|
|||||||
int get_top_group(); // used by ffield
|
int get_top_group(); // used by ffield
|
||||||
int top_group; // used by ffield
|
int top_group; // used by ffield
|
||||||
bool tfflag;
|
bool tfflag;
|
||||||
|
int eta_index; // index of atom property for eta
|
||||||
|
bool etaflag; // eta specified as atom property
|
||||||
bool timer_flag;
|
bool timer_flag;
|
||||||
std::map<int, double> tf_types;
|
std::map<int, double> tf_types;
|
||||||
// cg
|
// cg
|
||||||
@ -142,6 +149,9 @@ class FixElectrodeConp : public Fix {
|
|||||||
std::vector<double> gather_ngroup(std::vector<double>);
|
std::vector<double> gather_ngroup(std::vector<double>);
|
||||||
std::vector<double> gather_elevec_local(ElectrodeVector *);
|
std::vector<double> gather_elevec_local(ElectrodeVector *);
|
||||||
void set_charges(std::vector<double>);
|
void set_charges(std::vector<double>);
|
||||||
|
// qtotal
|
||||||
|
double macro_capacitance_sum;
|
||||||
|
void update_psi_qtotal();
|
||||||
|
|
||||||
// fix-specific electrode ID storage system:
|
// fix-specific electrode ID storage system:
|
||||||
|
|
||||||
|
|||||||
@ -30,7 +30,7 @@ FixElectrodeConq::FixElectrodeConq(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
FixElectrodeConp(lmp, narg, arg)
|
FixElectrodeConp(lmp, narg, arg)
|
||||||
{
|
{
|
||||||
// copy const-style values across because update_psi will change group_psi
|
// copy const-style values across because update_psi will change group_psi
|
||||||
group_q = group_psi;
|
group_q = group_psi_const;
|
||||||
|
|
||||||
if (symm) {
|
if (symm) {
|
||||||
if (num_of_groups == 1)
|
if (num_of_groups == 1)
|
||||||
|
|||||||
@ -47,7 +47,8 @@ FixElectrodeThermo::FixElectrodeThermo(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
if (thermo_time < SMALL) error->all(FLERR, "Keyword temp not set or zero in electrode/thermo");
|
if (thermo_time < SMALL) error->all(FLERR, "Keyword temp not set or zero in electrode/thermo");
|
||||||
|
|
||||||
thermo_random = new RanMars(lmp, thermo_init);
|
thermo_random = new RanMars(lmp, thermo_init);
|
||||||
if (group_psi_var_styles[0] == VarStyle::CONST) delta_psi_0 = group_psi[1] - group_psi[0];
|
if (group_psi_var_styles[0] == VarStyle::CONST)
|
||||||
|
delta_psi_0 = group_psi_const[1] - group_psi_const[0];
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------- */
|
/* ----------------------------------------------------------------------- */
|
||||||
@ -102,7 +103,7 @@ void FixElectrodeThermo::update_psi()
|
|||||||
double const delta_psi = group_psi_old[1] - group_psi_old[0];
|
double const delta_psi = group_psi_old[1] - group_psi_old[0];
|
||||||
|
|
||||||
// target potential difference from input parameters
|
// target potential difference from input parameters
|
||||||
if (group_psi_var_styles[0] != VarStyle::CONST) {
|
if (group_psi_var_styles[0] == VarStyle::EQUAL) {
|
||||||
delta_psi_0 = input->variable->compute_equal(group_psi_var_ids[1]) -
|
delta_psi_0 = input->variable->compute_equal(group_psi_var_ids[1]) -
|
||||||
input->variable->compute_equal(group_psi_var_ids[0]);
|
input->variable->compute_equal(group_psi_var_ids[0]);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -438,6 +438,7 @@ void PPPMElectrode::compute(int eflag, int vflag)
|
|||||||
|
|
||||||
start_compute();
|
start_compute();
|
||||||
|
|
||||||
|
/*
|
||||||
if (compute_vector_called && last_invert_source) {
|
if (compute_vector_called && last_invert_source) {
|
||||||
// electrolyte_density_brick is filled, so we can grab only electrode atoms.
|
// electrolyte_density_brick is filled, so we can grab only electrode atoms.
|
||||||
// Does not work for direct cg algorithm because electrode charges change after compute_vector.
|
// Does not work for direct cg algorithm because electrode charges change after compute_vector.
|
||||||
@ -453,15 +454,17 @@ void PPPMElectrode::compute(int eflag, int vflag)
|
|||||||
density_brick[nz][ny][nx] += electrolyte_density_brick[nz][ny][nx];
|
density_brick[nz][ny][nx] += electrolyte_density_brick[nz][ny][nx];
|
||||||
}
|
}
|
||||||
} else {
|
} else {
|
||||||
make_rho();
|
*/
|
||||||
|
particle_map();
|
||||||
|
make_rho();
|
||||||
|
|
||||||
// all procs communicate density values from their ghost cells
|
// all procs communicate density values from their ghost cells
|
||||||
// to fully sum contribution in their 3d bricks
|
// to fully sum contribution in their 3d bricks
|
||||||
// remap from 3d decomposition to FFT decomposition
|
// remap from 3d decomposition to FFT decomposition
|
||||||
|
|
||||||
gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2,
|
gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2,
|
||||||
MPI_FFT_SCALAR);
|
MPI_FFT_SCALAR);
|
||||||
}
|
//}
|
||||||
|
|
||||||
brick2fft();
|
brick2fft();
|
||||||
|
|
||||||
@ -584,6 +587,7 @@ void PPPMElectrode::compute_vector(double *vec, int sensor_grpbit, int source_gr
|
|||||||
// electrolyte density (without writing an additional function)
|
// electrolyte density (without writing an additional function)
|
||||||
FFT_SCALAR ***density_brick_real = density_brick;
|
FFT_SCALAR ***density_brick_real = density_brick;
|
||||||
FFT_SCALAR *density_fft_real = density_fft;
|
FFT_SCALAR *density_fft_real = density_fft;
|
||||||
|
particle_map();
|
||||||
make_rho_in_brick(source_grpbit, electrolyte_density_brick, invert_source);
|
make_rho_in_brick(source_grpbit, electrolyte_density_brick, invert_source);
|
||||||
density_brick = electrolyte_density_brick;
|
density_brick = electrolyte_density_brick;
|
||||||
density_fft = electrolyte_density_fft;
|
density_fft = electrolyte_density_fft;
|
||||||
@ -669,7 +673,8 @@ void PPPMElectrode::compute_matrix(bigint *imat, double **matrix, bool timer_fla
|
|||||||
// fft green's function k -> r (double)
|
// fft green's function k -> r (double)
|
||||||
double *greens_real;
|
double *greens_real;
|
||||||
memory->create(greens_real, nz_pppm * ny_pppm * nx_pppm, "pppm/electrode:greens_real");
|
memory->create(greens_real, nz_pppm * ny_pppm * nx_pppm, "pppm/electrode:greens_real");
|
||||||
memset(greens_real, 0, (std::size_t)nz_pppm * (std::size_t)ny_pppm * (std::size_t)nx_pppm * sizeof(double));
|
memset(greens_real, 0,
|
||||||
|
(std::size_t) nz_pppm * (std::size_t) ny_pppm * (std::size_t) nx_pppm * sizeof(double));
|
||||||
for (int i = 0, n = 0; i < nfft; i++) {
|
for (int i = 0, n = 0; i < nfft; i++) {
|
||||||
work2[n++] = greensfn[i];
|
work2[n++] = greensfn[i];
|
||||||
work2[n++] = ZEROF;
|
work2[n++] = ZEROF;
|
||||||
@ -862,7 +867,7 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, double *greens_real, d
|
|||||||
|
|
||||||
double **gw;
|
double **gw;
|
||||||
memory->create(gw, nmat, nxyz, "pppm/electrode:gw");
|
memory->create(gw, nmat, nxyz, "pppm/electrode:gw");
|
||||||
memset(&(gw[0][0]), 0, (std::size_t)nmat * (std::size_t)nxyz * sizeof(double));
|
memset(&(gw[0][0]), 0, (std::size_t) nmat * (std::size_t) nxyz * sizeof(double));
|
||||||
|
|
||||||
auto fmod = [](int x, int n) { // fast unsigned mod
|
auto fmod = [](int x, int n) { // fast unsigned mod
|
||||||
int r = abs(x);
|
int r = abs(x);
|
||||||
@ -981,17 +986,18 @@ void PPPMElectrode::allocate()
|
|||||||
// returns local owned and ghost grid bounds
|
// returns local owned and ghost grid bounds
|
||||||
// setup communication patterns and buffers
|
// setup communication patterns and buffers
|
||||||
|
|
||||||
gc = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
|
gc = new Grid3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_in, nxhi_in, nylo_in, nyhi_in,
|
||||||
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
|
nzlo_in, nzhi_in, nxlo_out, nxhi_out, nylo_out, nyhi_out, nzlo_out, nzhi_out);
|
||||||
nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out);
|
|
||||||
|
|
||||||
gc->setup_comm(ngc_buf1,ngc_buf2);
|
gc->setup_comm(ngc_buf1, ngc_buf2);
|
||||||
|
|
||||||
if (differentiation_flag) npergrid = 1;
|
if (differentiation_flag)
|
||||||
else npergrid = 3;
|
npergrid = 1;
|
||||||
|
else
|
||||||
|
npergrid = 3;
|
||||||
|
|
||||||
memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1");
|
memory->create(gc_buf1, npergrid * ngc_buf1, "pppm:gc_buf1");
|
||||||
memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2");
|
memory->create(gc_buf2, npergrid * ngc_buf2, "pppm:gc_buf2");
|
||||||
|
|
||||||
// tally local grid sizes
|
// tally local grid sizes
|
||||||
// ngrid = count of owned+ghost grid cells on this proc
|
// ngrid = count of owned+ghost grid cells on this proc
|
||||||
@ -1000,67 +1006,63 @@ void PPPMElectrode::allocate()
|
|||||||
// nfft = FFT points in x-pencil FFT decomposition on this proc
|
// nfft = FFT points in x-pencil FFT decomposition on this proc
|
||||||
// nfft_both = greater of nfft and nfft_brick
|
// nfft_both = greater of nfft and nfft_brick
|
||||||
|
|
||||||
ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
|
ngrid = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) * (nzhi_out - nzlo_out + 1);
|
||||||
(nzhi_out-nzlo_out+1);
|
|
||||||
|
|
||||||
nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) *
|
nfft_brick = (nxhi_in - nxlo_in + 1) * (nyhi_in - nylo_in + 1) * (nzhi_in - nzlo_in + 1);
|
||||||
(nzhi_in-nzlo_in+1);
|
|
||||||
|
|
||||||
nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) *
|
nfft = (nxhi_fft - nxlo_fft + 1) * (nyhi_fft - nylo_fft + 1) * (nzhi_fft - nzlo_fft + 1);
|
||||||
(nzhi_fft-nzlo_fft+1);
|
|
||||||
|
|
||||||
nfft_both = MAX(nfft,nfft_brick);
|
nfft_both = MAX(nfft, nfft_brick);
|
||||||
|
|
||||||
// allocate distributed grid data
|
// allocate distributed grid data
|
||||||
|
|
||||||
memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
memory->create3d_offset(density_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||||
nxlo_out,nxhi_out,"pppm:density_brick");
|
"pppm:density_brick");
|
||||||
|
|
||||||
memory->create(density_fft,nfft_both,"pppm:density_fft");
|
memory->create(density_fft, nfft_both, "pppm:density_fft");
|
||||||
memory->create(greensfn,nfft_both,"pppm:greensfn");
|
memory->create(greensfn, nfft_both, "pppm:greensfn");
|
||||||
memory->create(work1,2*nfft_both,"pppm:work1");
|
memory->create(work1, 2 * nfft_both, "pppm:work1");
|
||||||
memory->create(work2,2*nfft_both,"pppm:work2");
|
memory->create(work2, 2 * nfft_both, "pppm:work2");
|
||||||
memory->create(vg,nfft_both,6,"pppm:vg");
|
memory->create(vg, nfft_both, 6, "pppm:vg");
|
||||||
|
|
||||||
if (triclinic == 0) {
|
if (triclinic == 0) {
|
||||||
memory->create1d_offset(fkx,nxlo_fft,nxhi_fft,"pppm:fkx");
|
memory->create1d_offset(fkx, nxlo_fft, nxhi_fft, "pppm:fkx");
|
||||||
memory->create1d_offset(fky,nylo_fft,nyhi_fft,"pppm:fky");
|
memory->create1d_offset(fky, nylo_fft, nyhi_fft, "pppm:fky");
|
||||||
memory->create1d_offset(fkz,nzlo_fft,nzhi_fft,"pppm:fkz");
|
memory->create1d_offset(fkz, nzlo_fft, nzhi_fft, "pppm:fkz");
|
||||||
} else {
|
} else {
|
||||||
memory->create(fkx,nfft_both,"pppm:fkx");
|
memory->create(fkx, nfft_both, "pppm:fkx");
|
||||||
memory->create(fky,nfft_both,"pppm:fky");
|
memory->create(fky, nfft_both, "pppm:fky");
|
||||||
memory->create(fkz,nfft_both,"pppm:fkz");
|
memory->create(fkz, nfft_both, "pppm:fkz");
|
||||||
}
|
}
|
||||||
|
|
||||||
if (differentiation_flag == 1) {
|
if (differentiation_flag == 1) {
|
||||||
memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
memory->create3d_offset(u_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||||
nxlo_out,nxhi_out,"pppm:u_brick");
|
"pppm:u_brick");
|
||||||
|
|
||||||
memory->create(sf_precoeff1,nfft_both,"pppm:sf_precoeff1");
|
memory->create(sf_precoeff1, nfft_both, "pppm:sf_precoeff1");
|
||||||
memory->create(sf_precoeff2,nfft_both,"pppm:sf_precoeff2");
|
memory->create(sf_precoeff2, nfft_both, "pppm:sf_precoeff2");
|
||||||
memory->create(sf_precoeff3,nfft_both,"pppm:sf_precoeff3");
|
memory->create(sf_precoeff3, nfft_both, "pppm:sf_precoeff3");
|
||||||
memory->create(sf_precoeff4,nfft_both,"pppm:sf_precoeff4");
|
memory->create(sf_precoeff4, nfft_both, "pppm:sf_precoeff4");
|
||||||
memory->create(sf_precoeff5,nfft_both,"pppm:sf_precoeff5");
|
memory->create(sf_precoeff5, nfft_both, "pppm:sf_precoeff5");
|
||||||
memory->create(sf_precoeff6,nfft_both,"pppm:sf_precoeff6");
|
memory->create(sf_precoeff6, nfft_both, "pppm:sf_precoeff6");
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
memory->create3d_offset(vdx_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||||
nxlo_out,nxhi_out,"pppm:vdx_brick");
|
"pppm:vdx_brick");
|
||||||
memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
memory->create3d_offset(vdy_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||||
nxlo_out,nxhi_out,"pppm:vdy_brick");
|
"pppm:vdy_brick");
|
||||||
memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
memory->create3d_offset(vdz_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||||
nxlo_out,nxhi_out,"pppm:vdz_brick");
|
"pppm:vdz_brick");
|
||||||
}
|
}
|
||||||
|
|
||||||
// summation coeffs
|
// summation coeffs
|
||||||
|
|
||||||
order_allocated = order;
|
order_allocated = order;
|
||||||
if (!stagger_flag) memory->create(gf_b,order,"pppm:gf_b");
|
if (!stagger_flag) memory->create(gf_b, order, "pppm:gf_b");
|
||||||
memory->create2d_offset(rho1d,3,-order/2,order/2,"pppm:rho1d");
|
memory->create2d_offset(rho1d, 3, -order / 2, order / 2, "pppm:rho1d");
|
||||||
memory->create2d_offset(drho1d,3,-order/2,order/2,"pppm:drho1d");
|
memory->create2d_offset(drho1d, 3, -order / 2, order / 2, "pppm:drho1d");
|
||||||
memory->create2d_offset(rho_coeff,order,(1-order)/2,order/2,"pppm:rho_coeff");
|
memory->create2d_offset(rho_coeff, order, (1 - order) / 2, order / 2, "pppm:rho_coeff");
|
||||||
memory->create2d_offset(drho_coeff,order,(1-order)/2,order/2,
|
memory->create2d_offset(drho_coeff, order, (1 - order) / 2, order / 2, "pppm:drho_coeff");
|
||||||
"pppm:drho_coeff");
|
|
||||||
|
|
||||||
// create 2 FFTs and a Remap
|
// create 2 FFTs and a Remap
|
||||||
// 1st FFT keeps data in FFT decomposition
|
// 1st FFT keeps data in FFT decomposition
|
||||||
@ -1069,20 +1071,17 @@ void PPPMElectrode::allocate()
|
|||||||
|
|
||||||
int tmp;
|
int tmp;
|
||||||
|
|
||||||
fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
|
fft1 = new FFT3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_fft, nxhi_fft, nylo_fft, nyhi_fft,
|
||||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
nzlo_fft, nzhi_fft, nxlo_fft, nxhi_fft, nylo_fft, nyhi_fft, nzlo_fft, nzhi_fft,
|
||||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
0, 0, &tmp, collective_flag);
|
||||||
0,0,&tmp,collective_flag);
|
|
||||||
|
|
||||||
fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
|
fft2 = new FFT3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_fft, nxhi_fft, nylo_fft, nyhi_fft,
|
||||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
nzlo_fft, nzhi_fft, nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, 0, 0,
|
||||||
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
|
&tmp, collective_flag);
|
||||||
0,0,&tmp,collective_flag);
|
|
||||||
|
|
||||||
remap = new Remap(lmp,world,
|
remap = new Remap(lmp, world, nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, nxlo_fft,
|
||||||
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
|
nxhi_fft, nylo_fft, nyhi_fft, nzlo_fft, nzhi_fft, 1, 0, 0, FFT_PRECISION,
|
||||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
collective_flag);
|
||||||
1,0,0,FFT_PRECISION,collective_flag);
|
|
||||||
|
|
||||||
// ELECTRODE specific allocations
|
// ELECTRODE specific allocations
|
||||||
|
|
||||||
|
|||||||
@ -22,3 +22,4 @@ angle_coeff *
|
|||||||
|
|
||||||
group bot type 1
|
group bot type 1
|
||||||
group top type 2
|
group top type 2
|
||||||
|
group ele type 1 2
|
||||||
|
|||||||
@ -1,6 +1,6 @@
|
|||||||
---
|
---
|
||||||
lammps_version: 23 Jun 2022
|
lammps_version: 7 Feb 2024
|
||||||
date_generated: Wed Sep 21 13:52:53 2022
|
date_generated: Mon Mar 4 09:44:30 2024
|
||||||
epsilon: 1e-12
|
epsilon: 1e-12
|
||||||
skip_tests: gpu kokkos_omp omp
|
skip_tests: gpu kokkos_omp omp
|
||||||
prerequisites: ! |
|
prerequisites: ! |
|
||||||
@ -16,6 +16,7 @@ post_commands: ! |
|
|||||||
kspace_modify gewald 0.23118
|
kspace_modify gewald 0.23118
|
||||||
kspace_modify slab ew2d
|
kspace_modify slab ew2d
|
||||||
fix fxcpm bot electrode/conp -1.0 1.805 couple top 1.0 symm on
|
fix fxcpm bot electrode/conp -1.0 1.805 couple top 1.0 symm on
|
||||||
|
fix fxforce ele setforce 0 0 0
|
||||||
input_file: in.conp
|
input_file: in.conp
|
||||||
pair_style: coul/long 15.0
|
pair_style: coul/long 15.0
|
||||||
pair_coeff: ! |
|
pair_coeff: ! |
|
||||||
@ -27,97 +28,97 @@ init_coul: 2.215589572896434
|
|||||||
init_stress: ! |2-
|
init_stress: ! |2-
|
||||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
init_forces: ! |2
|
init_forces: ! |2
|
||||||
1 2.0780648532795694e-04 1.9949672015209204e-03 3.1005914149473996e+00
|
1 2.0780648532797705e-04 1.9949672015210172e-03 3.1005914149473988e+00
|
||||||
2 -1.6777235182686288e-02 2.1481432256290419e-03 3.0881659196467988e+00
|
2 -1.6777235182686239e-02 2.1481432256291962e-03 3.0881659196467979e+00
|
||||||
3 6.0082164895554737e-04 5.1573260226633801e-03 3.1029192412328555e+00
|
3 6.0082164895566240e-04 5.1573260226632518e-03 3.1029192412328550e+00
|
||||||
4 -1.6728974802490675e-02 6.1174723156886242e-03 3.0909324782862346e+00
|
4 -1.6728974802490665e-02 6.1174723156885227e-03 3.0909324782862333e+00
|
||||||
5 4.2029366155132378e-02 -2.3455526736195693e-03 -1.5659617577954634e+00
|
5 4.2029366155132364e-02 -2.3455526736195940e-03 -1.5659617577954636e+00
|
||||||
6 5.5635790919204904e-02 -2.4542947062522369e-03 -1.5693827709331334e+00
|
6 5.5635790919204904e-02 -2.4542947062522933e-03 -1.5693827709331336e+00
|
||||||
7 4.2014920784252008e-02 -7.5287470219125008e-04 -1.5671265392163820e+00
|
7 4.2014920784251980e-02 -7.5287470219118655e-04 -1.5671265392163822e+00
|
||||||
8 5.5808767852333470e-02 -9.9105389808573120e-04 -1.5707104957299389e+00
|
8 5.5808767852333491e-02 -9.9105389808568046e-04 -1.5707104957299391e+00
|
||||||
9 -5.0959878750421551e-02 -2.3630298689785601e-03 -1.5769250181497101e+00
|
9 -5.0959878750421538e-02 -2.3630298689785965e-03 -1.5769250181497101e+00
|
||||||
10 -3.3526564930579039e-02 -2.3802275431282884e-03 -1.5617801011657175e+00
|
10 -3.3526564930579081e-02 -2.3802275431283552e-03 -1.5617801011657175e+00
|
||||||
11 -5.1236396351794389e-02 -4.9531100598979201e-04 -1.5779995894034005e+00
|
11 -5.1236396351794437e-02 -4.9531100598972577e-04 -1.5779995894034005e+00
|
||||||
12 -3.3740693032952060e-02 -1.0210406243572182e-03 -1.5630986537874150e+00
|
12 -3.3740693032952088e-02 -1.0210406243571744e-03 -1.5630986537874152e+00
|
||||||
13 -1.1437102611353016e-03 -4.6454866413029015e-05 5.4282837980149448e-03
|
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
14 2.3914999373115431e-03 -1.6478680244651469e-04 2.9802178734319239e-02
|
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
15 3.9287193302652786e-05 -2.5715673267285659e-05 2.8944525105129479e-03
|
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
16 2.0458480716482328e-03 -1.2119161321908735e-04 3.3689550843809452e-02
|
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
17 -2.7146073277767471e-03 -8.2376243258224663e-04 2.6564130941474612e-02
|
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
18 1.3669692885198135e-03 -4.2357196145489820e-04 3.2396141113926739e-02
|
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
19 3.0143371860819995e-04 -8.6218593339583785e-04 2.6284521141350669e-02
|
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
20 1.1542435168435056e-03 -2.7252318260838826e-04 3.4237916528138110e-02
|
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
21 -1.2350056952573553e-03 4.8655691135364269e-04 5.9284283442393631e-03
|
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
22 2.3656743884722890e-03 9.6575340844312705e-04 2.9811074931784823e-02
|
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
23 4.6754986244969657e-05 3.0149464050350903e-04 3.4630785686112129e-03
|
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
24 2.0301227080749633e-03 6.3879578068684812e-04 3.3653437189053413e-02
|
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
25 -2.3656211013513076e-03 -8.0454594828768334e-04 2.8476980555362911e-02
|
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
26 1.1566723797447039e-03 -3.9614599888570504e-04 3.2873323713155905e-02
|
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
27 2.8784994028036400e-04 -8.3661697184444898e-04 2.8317655886021253e-02
|
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
28 9.3882364605486020e-04 -2.3327601777843495e-04 3.4334676606415648e-02
|
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
29 -4.7969977052124917e-04 -1.2933334305373028e-04 -1.2336987392568071e-02
|
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
30 6.4733118786851766e-05 -1.3190918849005797e-04 -1.2737933567178844e-02
|
30 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
31 2.4269094157913586e-04 -1.3093943526788584e-04 -1.2136133260085013e-02
|
31 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
32 1.7452552740941527e-04 -1.1792779046242341e-04 -1.4181538324619835e-02
|
32 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
33 -3.8366266481516803e-04 -7.1061854758754556e-05 -1.3699106365426135e-02
|
33 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
34 2.8849004082563746e-05 -5.7838605310673531e-05 -1.3764181266896890e-02
|
34 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
35 2.2648059665862587e-04 -7.2851385190891320e-05 -1.3537361892926607e-02
|
35 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
36 1.2929221129083645e-04 -4.2862960950045859e-05 -1.4926105930886896e-02
|
36 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
37 -4.7698025941707008e-04 2.9971529466656788e-04 -1.2393604822896313e-02
|
37 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
38 6.4231095731188766e-05 2.7548977518460050e-04 -1.2789498345723021e-02
|
38 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
39 2.4169204779864826e-04 3.0552093685810269e-04 -1.2193908285665961e-02
|
39 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
40 1.7324998349441456e-04 2.2898000918153004e-04 -1.4225267020837207e-02
|
40 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
41 -3.4345772150395188e-04 -9.8012060153887415e-05 -1.4482722052972283e-02
|
41 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
42 2.0345466940577010e-05 -8.5250083485342566e-05 -1.4497101004472062e-02
|
42 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
43 2.0917627239292995e-04 -1.0051271468149899e-04 -1.4335313646556430e-02
|
43 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
44 1.1456796622437295e-04 -6.7553675788598551e-05 -1.5543196158604005e-02
|
44 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
run_vdwl: 0
|
run_vdwl: 0
|
||||||
run_coul: 6.662694629990089
|
run_coul: 6.662694556930397
|
||||||
run_stress: ! |2-
|
run_stress: ! |2-
|
||||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
run_forces: ! |2
|
run_forces: ! |2
|
||||||
1 2.4590612609445102e-04 1.9614041218568861e-03 3.0874291949281147e+00
|
1 2.4590683616588566e-04 1.9614031577864796e-03 3.0874292323214036e+00
|
||||||
2 -1.6646393233505193e-02 2.1136941574790400e-03 3.0751132981100078e+00
|
2 -1.6646391056109287e-02 2.1136931488459688e-03 3.0751133344119794e+00
|
||||||
3 6.3535217476586373e-04 5.1012487117746350e-03 3.0897301317927290e+00
|
3 6.3535284261976926e-04 5.1012486499620825e-03 3.0897301693141319e+00
|
||||||
4 -1.6598677148313409e-02 6.0535154567108685e-03 3.0778495346381409e+00
|
4 -1.6598674977089559e-02 6.0535154273402107e-03 3.0778495712965124e+00
|
||||||
5 4.2257888534896988e-02 -2.3028533365965051e-03 -1.5593100596807521e+00
|
5 4.2257890248609438e-02 -2.3028528771736243e-03 -1.5593100743454236e+00
|
||||||
6 5.5690508027606708e-02 -2.4104721624763235e-03 -1.5626897542440843e+00
|
6 5.5690508840794850e-02 -2.4104716736066006e-03 -1.5626897684026868e+00
|
||||||
7 4.2243973130370149e-02 -7.6153220413259775e-04 -1.5604618260035832e+00
|
7 4.2243974848895645e-02 -7.6153214117129057e-04 -1.5604618407191602e+00
|
||||||
8 5.5862703939049158e-02 -9.9825803703216718e-04 -1.5640031014325448e+00
|
8 5.5862704771247280e-02 -9.9825804058299890e-04 -1.5640031157582626e+00
|
||||||
9 -5.1059409954744304e-02 -2.3195553026588347e-03 -1.5701677851024036e+00
|
9 -5.1059412079591346e-02 -2.3195548367148894e-03 -1.5701677996288432e+00
|
||||||
10 -3.3824298857146967e-02 -2.3375522139358631e-03 -1.5551647619109401e+00
|
10 -3.3824301875619085e-02 -2.3375517362837230e-03 -1.5551647759943836e+00
|
||||||
11 -5.1334079184640377e-02 -5.0583705005136689e-04 -1.5712298444761112e+00
|
11 -5.1334081278836916e-02 -5.0583707575582921e-04 -1.5712298590599834e+00
|
||||||
12 -3.4037363466305925e-02 -1.0275978089057873e-03 -1.5564691026885336e+00
|
12 -3.4037366496628307e-02 -1.0275977984217173e-03 -1.5564691169384559e+00
|
||||||
13 -1.1767076011504501e-03 -4.7681963272732406e-05 5.6177800544716262e-03
|
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
14 2.3826294437743331e-03 -1.6349140124449633e-04 2.9836275824428962e-02
|
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
15 4.1635367214843796e-05 -2.7287283914685102e-05 3.0967012748694773e-03
|
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
16 2.0334138778396313e-03 -1.1986039772787527e-04 3.3679727731055195e-02
|
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
17 -2.7026084826568797e-03 -8.1815079485725360e-04 2.6574868248546435e-02
|
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
18 1.3603406762441243e-03 -4.1902595052936860e-04 3.2373613783594497e-02
|
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
19 2.9940467686436986e-04 -8.5646794759970863e-04 2.6296909514905095e-02
|
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
20 1.1469475577225402e-03 -2.6907093945665336e-04 3.4197589258157073e-02
|
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
21 -1.2662578686531134e-03 4.9770031968890231e-04 6.1141650873547037e-03
|
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
22 2.3568409810395020e-03 9.5671841592085381e-04 2.9844352492872490e-02
|
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
23 4.8965507374742117e-05 3.1616579858329929e-04 3.6613180489820005e-03
|
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
24 2.0177821554069170e-03 6.3083810187911310e-04 3.3643353017422439e-02
|
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
25 -2.3537455003017457e-03 -7.9846295760147956e-04 2.8468250829639500e-02
|
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
26 1.1507655048236000e-03 -3.9159985067612060e-04 3.2839870487003708e-02
|
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
27 2.8582562554448814e-04 -8.3038492818152999e-04 2.8309777443009273e-02
|
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
28 9.3274285761092680e-04 -2.2997823984283208e-04 3.4287630335266286e-02
|
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
29 -4.7502414048888327e-04 -1.2847214455389489e-04 -1.2453998829891042e-02
|
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
30 6.3675154563755000e-05 -1.3104204562344653e-04 -1.2848240218511071e-02
|
30 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
31 2.4068203429808906e-04 -1.3007692195448562e-04 -1.2254443488117142e-02
|
31 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
32 1.7286880375665112e-04 -1.1713944254614034e-04 -1.4279748536149278e-02
|
32 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
33 -3.7975304094097439e-04 -7.0481503989778179e-05 -1.3805675914786045e-02
|
33 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
34 2.8172580422574018e-05 -5.7414812953860394e-05 -1.3867744309035916e-02
|
34 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
35 2.2448042926710853e-04 -7.2258368796568220e-05 -1.3645037267085249e-02
|
35 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
36 1.2804302797390986e-04 -4.2547023166907131e-05 -1.5019384166440140e-02
|
36 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
37 -4.7231656130619122e-04 2.9759414220405656e-04 -1.2510308090752414e-02
|
37 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
38 6.3181133759042352e-05 2.7366531591578288e-04 -1.2899551129187765e-02
|
38 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
39 2.3968383978790597e-04 3.0338116638639894e-04 -1.2311919409216509e-02
|
39 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
40 1.7159804905743131e-04 2.2744508340904917e-04 -1.4323246783684936e-02
|
40 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
41 -3.3986046011853923e-04 -9.7274166717457145e-05 -1.4583591616566860e-02
|
41 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
42 1.9775995840422978e-05 -8.4675117269364898e-05 -1.4595729099929700e-02
|
42 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
43 2.0725822207231137e-04 -9.9764702521265135e-05 -1.4437236974797743e-02
|
43 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
44 1.1345006523014360e-04 -6.7103771021504086e-05 -1.5632251527466189e-02
|
44 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
...
|
...
|
||||||
|
|||||||
@ -1,6 +1,6 @@
|
|||||||
---
|
---
|
||||||
lammps_version: 23 Jun 2022
|
lammps_version: 7 Feb 2024
|
||||||
date_generated: Wed Sep 21 13:52:39 2022
|
date_generated: Mon Mar 4 09:44:31 2024
|
||||||
epsilon: 3e-12
|
epsilon: 3e-12
|
||||||
skip_tests: gpu kokkos_omp omp
|
skip_tests: gpu kokkos_omp omp
|
||||||
prerequisites: ! |
|
prerequisites: ! |
|
||||||
@ -16,6 +16,7 @@ post_commands: ! |
|
|||||||
kspace_modify gewald 0.23118
|
kspace_modify gewald 0.23118
|
||||||
kspace_modify slab 3.0
|
kspace_modify slab 3.0
|
||||||
fix fxcpm bot electrode/conp -1.0 1.805 couple top 1.0 symm on
|
fix fxcpm bot electrode/conp -1.0 1.805 couple top 1.0 symm on
|
||||||
|
fix fxforce ele setforce 0 0 0
|
||||||
input_file: in.conp
|
input_file: in.conp
|
||||||
pair_style: coul/long 15.0
|
pair_style: coul/long 15.0
|
||||||
pair_coeff: ! |
|
pair_coeff: ! |
|
||||||
@ -23,101 +24,101 @@ pair_coeff: ! |
|
|||||||
extract: ! ""
|
extract: ! ""
|
||||||
natoms: 44
|
natoms: 44
|
||||||
init_vdwl: 0
|
init_vdwl: 0
|
||||||
init_coul: 2.2156402256727614
|
init_coul: 2.215640225672775
|
||||||
init_stress: ! |2-
|
init_stress: ! |2-
|
||||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
init_forces: ! |2
|
init_forces: ! |2
|
||||||
1 2.0996096688279944e-04 1.9837586784580306e-03 3.1004822661058822e+00
|
1 2.0996096688288336e-04 1.9837586784579777e-03 3.1004822661058866e+00
|
||||||
2 -1.6783332510617883e-02 2.1368843599407611e-03 3.0880130470329230e+00
|
2 -1.6783332510618088e-02 2.1368843599407052e-03 3.0880130470329270e+00
|
||||||
3 6.0300296042517466e-04 5.1688381279905342e-03 3.1028182137891114e+00
|
3 6.0300296042527755e-04 5.1688381279906869e-03 3.1028182137891140e+00
|
||||||
4 -1.6735061532950901e-02 6.1290626039690339e-03 3.0907879891042755e+00
|
4 -1.6735061532951116e-02 6.1290626039692056e-03 3.0907879891042778e+00
|
||||||
5 4.2014131860757913e-02 -2.3478381081742388e-03 -1.5658874682481487e+00
|
5 4.2014131860757857e-02 -2.3478381081742123e-03 -1.5658874682481501e+00
|
||||||
6 5.5659823770659422e-02 -2.4566144388410410e-03 -1.5693278833316506e+00
|
6 5.5659823770659547e-02 -2.4566144388410201e-03 -1.5693278833316524e+00
|
||||||
7 4.1999624791768865e-02 -7.5066218795240259e-04 -1.5670569809441617e+00
|
7 4.1999624791768810e-02 -7.5066218795247393e-04 -1.5670569809441637e+00
|
||||||
8 5.5832732887661884e-02 -9.8883264742169940e-04 -1.5706605160409139e+00
|
8 5.5832732887661961e-02 -9.8883264742177161e-04 -1.5706605160409157e+00
|
||||||
9 -5.0976953599115804e-02 -2.3653810185280950e-03 -1.5768945194236066e+00
|
9 -5.0976953599115846e-02 -2.3653810185280759e-03 -1.5768945194236084e+00
|
||||||
10 -3.3513771125456657e-02 -2.3824712764543426e-03 -1.5616806812004886e+00
|
10 -3.3513771125456573e-02 -2.3824712764543218e-03 -1.5616806812004898e+00
|
||||||
11 -5.1253442064492741e-02 -4.9304425051529275e-04 -1.5779738349804424e+00
|
11 -5.1253442064492769e-02 -4.9304425051536007e-04 -1.5779738349804435e+00
|
||||||
12 -3.3727836471637192e-02 -1.0188844490582761e-03 -1.5630041309277038e+00
|
12 -3.3727836471637081e-02 -1.0188844490583557e-03 -1.5630041309277052e+00
|
||||||
13 -1.1453068449918257e-03 -4.7335833322794788e-05 5.4292779404649470e-03
|
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
14 2.3900993287279790e-03 -1.6878550058260119e-04 2.9808528147740175e-02
|
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
15 4.0078428215627730e-05 -2.6184607051201481e-05 2.8941780231019881e-03
|
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
16 2.0473353699190459e-03 -1.2552209515766962e-04 3.3684989110502959e-02
|
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
17 -2.7210216747431955e-03 -8.2349543008294359e-04 2.6567504438257068e-02
|
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
18 1.3656002828979516e-03 -4.2323438710338486e-04 3.2404938547366383e-02
|
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
19 3.0785575286292939e-04 -8.6186674263511191e-04 2.6288541663855129e-02
|
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
20 1.1555469330548321e-03 -2.7230960410720359e-04 3.4235148032534163e-02
|
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
21 -1.2368093613861506e-03 4.8760847861882366e-04 5.9296798954256557e-03
|
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
22 2.3643140421916085e-03 9.6975102599399746e-04 2.9817231402721564e-02
|
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
23 4.7705653522709085e-05 3.0203836842154655e-04 3.4631818106649337e-03
|
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
24 2.0316297431160258e-03 6.4335031755788927e-04 3.3648629802522749e-02
|
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
25 -2.3728144718995455e-03 -8.0497592536520339e-04 2.8474707915345274e-02
|
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
26 1.1555985481661916e-03 -3.9649433660109970e-04 3.2876098209196375e-02
|
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
27 2.9459292459149998e-04 -8.3700881746301306e-04 2.8316136079038545e-02
|
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
28 9.4027352090446912e-04 -2.3371025598546553e-04 3.4325153603153732e-02
|
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
29 -5.2133856931286127e-04 -1.4498587872629142e-04 -1.2345168780426297e-02
|
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
30 7.0344538924238829e-05 -1.4805754895657979e-04 -1.2765142487049358e-02
|
30 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
31 2.7857644686035687e-04 -1.4667349483298643e-04 -1.2140095836769501e-02
|
31 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
32 1.7479865631996218e-04 -1.3335074368636031e-04 -1.4152171307753206e-02
|
32 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
33 -4.2607366742485959e-04 -7.2661709209033136e-05 -1.3713642029394900e-02
|
33 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
34 3.4224570995904750e-05 -5.9352423088202727e-05 -1.3797063100154012e-02
|
34 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
35 2.6332638434852483e-04 -7.4573909050170201e-05 -1.3548481212572565e-02
|
35 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
36 1.2956589882656260e-04 -4.4469640559387641e-05 -1.4903750420442119e-02
|
36 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
37 -5.1855202137555164e-04 3.1768672664149645e-04 -1.2402413876588990e-02
|
37 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
38 6.9744637010106164e-05 2.9379923413403201e-04 -1.2817238930047764e-02
|
38 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
39 2.7753815671547851e-04 3.2364879063853462e-04 -1.2198687630220518e-02
|
39 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
40 1.7359211286247436e-04 2.4661766514410969e-04 -1.4196607980261094e-02
|
40 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
41 -3.8501793941197521e-04 -9.8818538537990245e-05 -1.4472863167957050e-02
|
41 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
42 2.5779944975443997e-05 -8.5975255466014692e-05 -1.4504933662725301e-02
|
42 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
43 2.4535595442148292e-04 -1.0127263490049206e-04 -1.4321758087878972e-02
|
43 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
44 1.1457678622968817e-04 -6.8200688092186871e-05 -1.5499407046729242e-02
|
44 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
run_vdwl: 0
|
run_vdwl: 0
|
||||||
run_coul: 6.662844717848837
|
run_coul: 6.662844644802024
|
||||||
run_stress: ! |2-
|
run_stress: ! |2-
|
||||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
run_forces: ! |2
|
run_forces: ! |2
|
||||||
1 2.4838374656870440e-04 1.9503798034564181e-03 3.0873204052231675e+00
|
1 2.4838446863956616e-04 1.9503788466163226e-03 3.0873204426106526e+00
|
||||||
2 -1.6652792550963507e-02 2.1026197438206527e-03 3.0749612313228378e+00
|
2 -1.6652790386577014e-02 2.1026187422225435e-03 3.0749612676149027e+00
|
||||||
3 6.3785681925848106e-04 5.1125747842690368e-03 3.0896293583134606e+00
|
3 6.3785749905510489e-04 5.1125747155211397e-03 3.0896293958296610e+00
|
||||||
4 -1.6605065971975488e-02 6.0649203428150876e-03 3.0777057441315305e+00
|
4 -1.6605063813845172e-02 6.0649203065202620e-03 3.0777057807809554e+00
|
||||||
5 4.2242720963296274e-02 -2.3050719334346786e-03 -1.5592361839228894e+00
|
5 4.2242722672783749e-02 -2.3050714764837649e-03 -1.5592361985876177e+00
|
||||||
6 5.5714272244614366e-02 -2.4127241272198356e-03 -1.5626351053810128e+00
|
6 5.5714273062644336e-02 -2.4127236407636803e-03 -1.5626351195306318e+00
|
||||||
7 4.2228744507856318e-02 -7.5938680980830215e-04 -1.5603926173148708e+00
|
7 4.2228746222139832e-02 -7.5938674438442760e-04 -1.5603926320308752e+00
|
||||||
8 5.5886400463161408e-02 -9.9610508394880446e-04 -1.5639532943562677e+00
|
8 5.5886401300220948e-02 -9.9610508505008281e-04 -1.5639533086735800e+00
|
||||||
9 -5.1076260774663269e-02 -2.3218376339398856e-03 -1.5701372580807029e+00
|
9 -5.1076262902731158e-02 -2.3218371704875301e-03 -1.5701372726008263e+00
|
||||||
10 -3.3811558405906099e-02 -2.3397301017438945e-03 -1.5550660295253020e+00
|
10 -3.3811561421032657e-02 -2.3397296264742822e-03 -1.5550660436064543e+00
|
||||||
11 -5.1350900750795785e-02 -5.0363945411724615e-04 -1.5712039970018119e+00
|
11 -5.1350902848165500e-02 -5.0363947736732217e-04 -1.5712040115797643e+00
|
||||||
12 -3.4024561045577786e-02 -1.0255079139096881e-03 -1.5563752017113657e+00
|
12 -3.4024564072498521e-02 -1.0255079009805182e-03 -1.5563752159595889e+00
|
||||||
13 -1.1783355827329363e-03 -4.8584425213699084e-05 5.6187810005819084e-03
|
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
14 2.3812433011153062e-03 -1.6745821939573657e-04 2.9842604329757397e-02
|
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
15 4.2472634867315832e-05 -2.7784504406519571e-05 3.0964622176844602e-03
|
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
16 2.0348857368272344e-03 -1.2415016403438035e-04 3.3675205082768264e-02
|
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
17 -2.7089567432503573e-03 -8.1788662401764114e-04 2.6578231998707000e-02
|
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
18 1.3589859834844708e-03 -4.1869284075205220e-04 3.2382362625908642e-02
|
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
19 3.0575998684987288e-04 -8.5615261685325662e-04 2.6300918365183709e-02
|
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
20 1.1482382726252934e-03 -2.6885864047674810e-04 3.4194853807722227e-02
|
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
21 -1.2680891310638792e-03 4.9877122346546224e-04 6.1154164862940522e-03
|
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
22 2.3554944751877239e-03 9.6068685589809240e-04 2.9850487598267021e-02
|
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
23 4.9959016556344255e-05 3.1673714227676154e-04 3.6614479955528112e-03
|
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
24 2.0192733259603224e-03 6.3534849028298586e-04 3.3638585635455770e-02
|
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
25 -2.3608563352120440e-03 -7.9888874314704573e-04 2.8465994834953420e-02
|
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
26 1.1497012824588045e-03 -3.9194609517719160e-04 3.2842627585052867e-02
|
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
27 2.9249325092285189e-04 -8.3077344407106490e-04 2.8308269755484061e-02
|
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
28 9.3417705968603434e-04 -2.3040781495046246e-04 3.4278191255128133e-02
|
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
29 -5.1652528928022433e-04 -1.4404353042683099e-04 -1.2462150875064196e-02
|
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
30 6.9288940488795056e-05 -1.4710788156542239e-04 -1.2875332550432134e-02
|
30 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
31 2.7644608312646314e-04 -1.4573040212804145e-04 -1.2258366148270420e-02
|
31 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
32 1.7312052380602741e-04 -1.3246895843787418e-04 -1.4250473428514749e-02
|
32 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
33 -4.2201273060055557e-04 -7.2075937985441126e-05 -1.3820153961237609e-02
|
33 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
34 3.3549241776445280e-05 -5.8924381188893540e-05 -1.3900492261623465e-02
|
34 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
35 2.6119063773180797e-04 -7.3975274656908229e-05 -1.3656086631368676e-02
|
35 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
36 1.2829798186810219e-04 -4.4146305074977061e-05 -1.4997087695938056e-02
|
36 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
37 -5.1375024459660446e-04 3.1547360096919003e-04 -1.2519087424517190e-02
|
37 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
38 6.8697062203298403e-05 2.9188411177715840e-04 -1.2927175328444108e-02
|
38 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
39 2.7540798890579723e-04 3.2141722701930868e-04 -1.2316658300695350e-02
|
39 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
40 1.7191884579607650e-04 2.4497453169432579e-04 -1.4294679585099376e-02
|
40 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
41 -3.8125358429239129e-04 -9.8073404256391242e-05 -1.4573806404289218e-02
|
41 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
42 2.5208712883704254e-05 -8.5394829999053783e-05 -1.4603558816163261e-02
|
42 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
43 2.4329125095209453e-04 -1.0051714757303402e-04 -1.4423743772053488e-02
|
43 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
44 1.1343880007511943e-04 -6.7742613833467660e-05 -1.5588639087563531e-02
|
44 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||||
...
|
...
|
||||||
|
|||||||
Reference in New Issue
Block a user