Merge pull request #4095 from robeme/electrode
Update for the ELECTRODE package
This commit is contained in:
Axel Kohlmeyer
@ -45,7 +45,7 @@ Syntax
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rng_v = integer used to initialize random number generator
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* zero or more keyword/value pairs may be appended
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* keyword = *algo* or *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv*
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* 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*
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.. parsed-literal::
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@ -68,6 +68,10 @@ Syntax
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filename = file from which to read elastance matrix
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*read_inv* value = filename
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filename = file from which to read inverted matrix
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*qtotal* value = number or *v_* equal-style variable
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add overall potential so that all electrode charges add up to *qtotal*
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*eta* value = d_propname
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d_propname = a custom double vector defined via fix property/atom
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Examples
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""""""""
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@ -249,6 +253,24 @@ be enabled if any electrode particle has the same type as any
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electrolyte particle (which would be unusual in a typical simulation)
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and the fix will issue an error in that case.
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.. versionchanged:: qtotal
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The keyword *qtotal* causes *fix electrode/conp* and *fix electrode/thermo*
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to add an overall potential to all electrodes so that the total charge on
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the electrodes is a specified amount (which may be an equal-style variable).
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For example, if a user wanted to simulate a solution of excess cations
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such that the total electrolyte charge is +2, setting *qtotal -2* would cause
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the total electrode charge to be -2, so that the simulation box remains overall
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electroneutral. Since *fix electrode/conq* constrains the total charges of
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individual electrodes, and since *symm on* constrains the total charge of all
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electrodes to be zero, either option is incompatible with the *qtotal* keyword
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(even if *qtotal* is set to zero).
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The keyword *eta* takes the name of a custom double vector defined via fix
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property/atom. The values will be used instead of the standard eta value. The
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property/atom fix must be for vector of double values and use the *ghost on*
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option.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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@ -1,7 +1,7 @@
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#!/usr/env/python3
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import sys
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import os.path as op
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import sys
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def rel_error(out, ref):
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@ -49,5 +49,5 @@ for label, ref, out in out_lines:
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error = rel_error(out, ref)
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lines.append(f"{label}: {out:.5f}, {error:.5f}\n")
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with open("madelung.txt", 'a') as f:
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with open("madelung.txt", "a") as f:
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f.writelines(lines)
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14
examples/PACKAGES/electrode/madelung/in.eta
Normal file
14
examples/PACKAGES/electrode/madelung/in.eta
Normal file
@ -0,0 +1,14 @@
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boundary p p f
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kspace_style ewald/electrode 1.0e-8
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kspace_modify slab 8.0 # ew3dc
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include "settings.mod" # styles, computes, groups and fixes
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thermo_style custom step pe c_qbot c_qtop
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fix feta all property/atom d_eta ghost on
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set group bot d_eta 2.0
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set group top d_eta 2.0
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fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
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run 0
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14
examples/PACKAGES/electrode/madelung/in.eta_cg
Normal file
14
examples/PACKAGES/electrode/madelung/in.eta_cg
Normal file
@ -0,0 +1,14 @@
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boundary p p f
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kspace_style ewald/electrode 1.0e-8
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kspace_modify slab 8.0 # ew3dc
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include "settings.mod" # styles, computes, groups and fixes
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thermo_style custom step pe c_qbot c_qtop
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fix feta all property/atom d_eta ghost on
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set group bot d_eta 0.5
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set group top d_eta 3.0
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fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6
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run 0
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14
examples/PACKAGES/electrode/madelung/in.eta_mix
Normal file
14
examples/PACKAGES/electrode/madelung/in.eta_mix
Normal file
@ -0,0 +1,14 @@
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boundary p p f
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kspace_style ewald/electrode 1.0e-8
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kspace_modify slab 8.0 # ew3dc
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include "settings.mod" # styles, computes, groups and fixes
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thermo_style custom step pe c_qbot c_qtop
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fix feta all property/atom d_eta ghost on
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set group bot d_eta 0.5
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set group top d_eta 3.0
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fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
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run 0
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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 @@
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-668-g5b6c0c6b56)
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using 1 OpenMP thread(s) per MPI task
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boundary p p f
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kspace_style ewald/electrode 1.0e-8
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kspace_modify slab 8.0 # ew3dc
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include "settings.mod" # styles, computes, groups and fixes
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# set boundary in main script because ffield is periodic
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units real
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# distribute electrode atoms among all processors:
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if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
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atom_style full
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pair_style lj/cut/coul/long 12
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read_data "data.au-elyt"
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Reading data file ...
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orthogonal box = (0 0 -10) to (1 1 10)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.003 seconds
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group bot type 1
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1 atoms in group bot
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group top type 2
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1 atoms in group top
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# get electrode charges
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variable q atom q
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compute qbot bot reduce sum v_q
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compute qtop top reduce sum v_q
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compute compute_pe all pe
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variable vpe equal c_compute_pe
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variable charge equal c_qtop
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fix fxprint all print 1 "${vpe}, ${charge}" file "out.csv"
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thermo_style custom step pe c_qbot c_qtop
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fix feta all property/atom d_eta ghost on
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set group bot d_eta 2.0
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Setting atom values ...
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1 settings made for d_eta
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set group top d_eta 2.0
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Setting atom values ...
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1 settings made for d_eta
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fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
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2 atoms in group conp_group
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run 0
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- fix electrode command:
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@article{Ahrens2022
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author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
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doi = {10.1063/5.0099239},
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title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
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journal = {The Journal of Chemical Physics},
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year = {2022}
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volume = {157},
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pages = {084801},
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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Ewald/electrode initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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WARNING: For better accuracy use 'pair_modify table 0' (src/kspace.cpp:365)
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G vector (1/distance) = 0.32261103
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estimated absolute RMS force accuracy = 3.8272011e-06
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estimated relative force accuracy = 1.1525502e-08
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KSpace vectors: actual max1d max3d = 52 50 515150
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kxmax kymax kzmax = 1 1 50
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Generated 3 of 3 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 1 1 3
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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(2) fix electrode/conp, perpetual, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:965)
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139.943964815502, 0.279214485147238
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Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.2 | 144.2 Mbytes
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Step PotEng c_qbot c_qtop
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0 139.94396 -0.27921449 0.27921449
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Loop time of 2.191e-06 on 1 procs for 0 steps with 4 atoms
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91.3% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Bond | 0 | 0 | 0 | 0.0 | 0.00
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Kspace | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 2.191e-06 | | |100.00
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Nlocal: 4 ave 4 max 4 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3596 ave 3596 max 3596 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 4790 ave 4790 max 4790 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 4790
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Ave neighs/atom = 1197.5
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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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 @@
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-668-g5b6c0c6b56)
|
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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
|
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.003 seconds
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group bot type 1
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1 atoms in group bot
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group top type 2
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1 atoms in group top
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# get electrode charges
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variable q atom q
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compute qbot bot reduce sum v_q
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compute qtop top reduce sum v_q
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|
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compute compute_pe all pe
|
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variable vpe equal c_compute_pe
|
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variable charge equal c_qtop
|
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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
|
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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
|
||||
from scipy.special import erf
|
||||
|
||||
ETA = 2
|
||||
SQRT2 = np.sqrt(2)
|
||||
COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units
|
||||
QE2F = 23.060549
|
||||
@ -17,14 +16,14 @@ def lattice(length):
|
||||
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"""
|
||||
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"""
|
||||
return q * erf(ETA * r) / r
|
||||
return q * erf(eta * r) / r
|
||||
|
||||
|
||||
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 = 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
|
||||
A_11 = np.sqrt(2 / np.pi) * ETA
|
||||
A_12 = erf(ETA * distance_plates / SQRT2) / distance_plates
|
||||
for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
|
||||
eta_mix = np.prod(eta_elec) / np.sqrt(np.sum(np.square(eta_elec)))
|
||||
# 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
|
||||
A_11 += 4 * np.sum(a_element(distances))
|
||||
A_12 += 4 * np.sum(a_element(opposite_distances))
|
||||
A = np.array([[A_11, A_12], [A_12, A_11]])
|
||||
inv = np.linalg.inv(A)
|
||||
e = np.array([1, 1])
|
||||
inv -= np.matmul(inv, np.matmul(np.outer(e, e), inv)) / np.dot(e, np.dot(inv, e))
|
||||
# interaction with periodic images
|
||||
A_11 += 4 * np.sum(a_element(distances, eta_elec[0] / SQRT2))
|
||||
A_22 += 4 * np.sum(a_element(distances, eta_elec[1] / SQRT2))
|
||||
A_12 += 4 * np.sum(a_element(opposite_distances, eta_mix))
|
||||
A = np.array([[A_11, A_12], [A_12, A_22]])
|
||||
inv = np.linalg.inv(A)
|
||||
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
|
||||
b = []
|
||||
for x in x_elec:
|
||||
bi = 0
|
||||
for y, q in zip(x_elyt, q_elyt):
|
||||
d = abs(y - x)
|
||||
bi += b_element(d, q)
|
||||
image_distances = np.sqrt(np.square(distances) + d ** 2)
|
||||
bi += 4 * np.sum(b_element(image_distances, q))
|
||||
b.append(bi)
|
||||
b = np.array(b)
|
||||
# electrode-electrolyte interaction
|
||||
b = []
|
||||
for x, eta in zip(x_elec, eta_elec):
|
||||
bi = 0
|
||||
for y, q in zip(x_elyt, q_elyt):
|
||||
d = abs(y - x)
|
||||
bi += b_element(d, q, eta)
|
||||
image_distances = np.sqrt(np.square(distances) + d**2)
|
||||
bi += 4 * np.sum(b_element(image_distances, q, eta))
|
||||
b.append(bi)
|
||||
b = np.array(b)
|
||||
|
||||
# electrolyte-electrolyte energy
|
||||
elyt_11 = 4 * np.sum(1 / distances)
|
||||
distance_elyt = x_elyt[1] - x_elyt[0]
|
||||
elyt_12 = 1 / distance_elyt + 4 * np.sum(
|
||||
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}",
|
||||
]
|
||||
# electrolyte-electrolyte energy
|
||||
elyt_11 = 4 * np.sum(1 / distances)
|
||||
distance_elyt = x_elyt[1] - x_elyt[0]
|
||||
elyt_12 = 1 / distance_elyt + 4 * np.sum(
|
||||
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)
|
||||
|
||||
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
|
||||
|
||||
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"
|
||||
python3 plate_cap.py > $ref_out
|
||||
python3 plate_cap.py
|
||||
fi
|
||||
|
||||
echo "Running Lammps inputs"
|
||||
# w/o eta mixing
|
||||
rm -rf madelung.txt && touch madelung.txt
|
||||
for file in in.*; do
|
||||
for file in in.eta in.ewald-ew3dc in.ewald-ew2d in.pppm-ew3dc in.cg; do
|
||||
printf "\n$file\n" >> madelung.txt
|
||||
rm -f out.csv inv.csv vec.csv
|
||||
$lmpbin -i $file &> /dev/null
|
||||
python3 eval.py $ref_out out.csv inv.csv vec.csv
|
||||
done
|
||||
|
||||
# with eta mixing
|
||||
for file in in.eta_mix in.eta_cg; do
|
||||
printf "\n$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
|
||||
|
||||
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
|
||||
#define LMP_ELECTRODE_MATH_H
|
||||
|
||||
#include "ewald_const.h"
|
||||
#include "math_const.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
using namespace EwaldConst;
|
||||
|
||||
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 double safe_erfc(double x)
|
||||
{
|
||||
if (x > ERFCMAX) return 0.;
|
||||
if (x > ERFCMAX) return 0.0;
|
||||
double expm2 = exp(-x * x);
|
||||
double t = 1.0 / (1.0 + EWALD_P * x);
|
||||
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)
|
||||
{
|
||||
if (x > ERFCMAX) {
|
||||
erfc = 0.;
|
||||
return 0.;
|
||||
erfc = 0.0;
|
||||
return 0.0;
|
||||
}
|
||||
double x2 = x * x;
|
||||
double expm2 = exp(-x2);
|
||||
double t = 1.0 / (1.0 + EWALD_P * x);
|
||||
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
|
||||
|
||||
|
||||
@ -43,6 +43,7 @@ ElectrodeMatrix::ElectrodeMatrix(LAMMPS *lmp, int electrode_group, double eta) :
|
||||
groupbit = group->bitmask[igroup];
|
||||
ngroup = group->count(igroup);
|
||||
this->eta = eta;
|
||||
etaflag = 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)
|
||||
{
|
||||
// setting all entries of coulomb matrix to zero
|
||||
@ -115,8 +124,6 @@ void ElectrodeMatrix::pair_contribution(double **array)
|
||||
int nlocal = atom->nlocal;
|
||||
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
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
@ -135,6 +142,7 @@ void ElectrodeMatrix::pair_contribution(double **array)
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta;
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
@ -152,6 +160,9 @@ void ElectrodeMatrix::pair_contribution(double **array)
|
||||
jtype = type[j];
|
||||
|
||||
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);
|
||||
rinv = 1.0 / r;
|
||||
aij = rinv;
|
||||
@ -178,7 +189,10 @@ void ElectrodeMatrix::self_contribution(double **array)
|
||||
const double preta = MY_SQRT2 / MY_PIS;
|
||||
|
||||
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);
|
||||
void setup(const std::unordered_map<tagint, int> &, class Pair *, class NeighList *);
|
||||
void setup_tf(const std::map<int, double> &);
|
||||
void setup_eta(int);
|
||||
void compute_array(double **, bool);
|
||||
int igroup;
|
||||
|
||||
@ -39,6 +40,8 @@ class ElectrodeMatrix : protected Pointers {
|
||||
double **cutsq;
|
||||
double g_ewald, eta;
|
||||
bool tfflag;
|
||||
bool etaflag;
|
||||
int eta_index;
|
||||
std::map<int, double> tf_types;
|
||||
std::unordered_map<tagint, int> tag_to_iele;
|
||||
bool assigned;
|
||||
|
||||
@ -29,6 +29,7 @@
|
||||
#include "neigh_list.h"
|
||||
#include "pair.h"
|
||||
|
||||
#include <cassert>
|
||||
#include <cmath>
|
||||
#include <exception>
|
||||
|
||||
@ -47,6 +48,7 @@ ElectrodeVector::ElectrodeVector(LAMMPS *lmp, int sensor_group, int source_group
|
||||
source_grpbit = group->bitmask[source_group];
|
||||
this->eta = eta;
|
||||
tfflag = false;
|
||||
etaflag = false;
|
||||
|
||||
kspace_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)
|
||||
{
|
||||
MPI_Barrier(world);
|
||||
@ -121,7 +131,6 @@ void ElectrodeVector::compute_vector(double *vector)
|
||||
|
||||
void ElectrodeVector::pair_contribution(double *vector)
|
||||
{
|
||||
double const etaij = eta * MY_ISQRT2;
|
||||
double **x = atom->x;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
@ -142,6 +151,7 @@ void ElectrodeVector::pair_contribution(double *vector)
|
||||
double const xtmp = x[i][0];
|
||||
double const ytmp = x[i][1];
|
||||
double const ztmp = x[i][2];
|
||||
double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta;
|
||||
int itype = type[i];
|
||||
int *jlist = firstneigh[i];
|
||||
int jnum = numneigh[i];
|
||||
@ -158,18 +168,22 @@ void ElectrodeVector::pair_contribution(double *vector)
|
||||
double const rsq = delx * delx + dely * dely + delz * delz;
|
||||
int jtype = type[j];
|
||||
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 rinv = 1.0 / r;
|
||||
double aij = rinv;
|
||||
aij *= ElectrodeMath::safe_erfc(g_ewald * r);
|
||||
if (invert_source)
|
||||
aij -= ElectrodeMath::safe_erfc(eta * r) * rinv;
|
||||
else
|
||||
aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv;
|
||||
if (i_in_sensor) {
|
||||
vector[i] += aij * q[j];
|
||||
//} else if (j_in_sensor) {
|
||||
}
|
||||
aij -= ElectrodeMath::safe_erfc(etaij * r) * rinv;
|
||||
if (i_in_sensor) { vector[i] += aij * q[j]; }
|
||||
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++) {
|
||||
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_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;
|
||||
void setup(class Pair *, class NeighList *, bool);
|
||||
void setup_tf(const std::map<int, double> &);
|
||||
void setup_eta(int);
|
||||
void compute_vector(double *);
|
||||
int igroup, source_group;
|
||||
|
||||
@ -39,6 +40,8 @@ class ElectrodeVector : protected Pointers {
|
||||
double **cutsq;
|
||||
double g_ewald, eta;
|
||||
bool tfflag;
|
||||
bool etaflag;
|
||||
int eta_index;
|
||||
std::map<int, double> tf_types;
|
||||
class Pair *pair;
|
||||
class NeighList *list;
|
||||
|
||||
@ -98,26 +98,30 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
||||
top_group = 0;
|
||||
intelflag = false;
|
||||
tfflag = false;
|
||||
etaflag = false;
|
||||
timer_flag = false;
|
||||
|
||||
update_time = 0;
|
||||
mult_time = 0;
|
||||
n_call = n_cg_step = 0;
|
||||
|
||||
qtotal = 0.;
|
||||
qtotal_var_style = VarStyle::UNSET;
|
||||
|
||||
// read fix command
|
||||
fixname = std::string(arg[0]);
|
||||
groups = std::vector<int>(1, igroup);
|
||||
group_bits = std::vector<int>(1, groupbit);
|
||||
group_psi_var_names = std::vector<std::string>(1);
|
||||
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;
|
||||
if (strstr(arg[3], "v_") == arg[3]) {
|
||||
std::string vname = arg[3];
|
||||
group_psi_var_names[0] = vname.substr(2);
|
||||
group_psi_var_styles[0] = VarStyle::EQUAL;
|
||||
} 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];
|
||||
eta = utils::numeric(FLERR, eta_str, false, lmp);
|
||||
int iarg = 5;
|
||||
@ -133,12 +137,12 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
||||
std::string vname = arg[iarg];
|
||||
group_psi_var_names.push_back(vname.substr(2));
|
||||
group_psi_var_styles.push_back(VarStyle::EQUAL);
|
||||
group_psi.push_back(0.);
|
||||
group_psi_const.push_back(0.);
|
||||
} else {
|
||||
std::string null;
|
||||
group_psi_var_names.push_back(null);
|
||||
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)) {
|
||||
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_time = utils::numeric(FLERR, arg[++iarg], false, lmp);
|
||||
thermo_init = utils::inumeric(FLERR, arg[++iarg], false, lmp);
|
||||
// toggle parameters
|
||||
} else if ((strcmp(arg[iarg], "etypes") == 0)) {
|
||||
} else if ((strcmp(arg[iarg], "qtotal") == 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);
|
||||
} else if ((strncmp(arg[iarg], "symm", 4) == 0)) {
|
||||
symm = utils::logical(FLERR, arg[++iarg], false, lmp);
|
||||
@ -209,6 +237,12 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
||||
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
|
||||
std::string union_group = "conp_group";
|
||||
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);
|
||||
assert(groups.size() == group_bits.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_names.size());
|
||||
assert(igroup == elyt_vector->igroup);
|
||||
@ -375,6 +410,31 @@ void FixElectrodeConp::init()
|
||||
if (strncmp(modify->fix[i]->style, "electrode", 9) == 0) count++;
|
||||
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
|
||||
if (etypes_neighlists)
|
||||
request_etypes_neighlists();
|
||||
@ -449,6 +509,7 @@ void FixElectrodeConp::setup_post_neighbor()
|
||||
// get equal-style variable ids:
|
||||
group_psi_var_ids = std::vector<int>(num_of_groups, -1);
|
||||
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;
|
||||
const char *var_name = group_psi_var_names[g].c_str();
|
||||
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);
|
||||
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:
|
||||
|
||||
evscale = force->qe2f / force->qqrd2e;
|
||||
elyt_vector->setup(pair, vec_neighlist, timer_flag);
|
||||
if (etaflag) elyt_vector->setup_eta(eta_index);
|
||||
if (need_elec_vector) {
|
||||
elec_vector->setup(pair, mat_neighlist, timer_flag);
|
||||
if (etaflag) elec_vector->setup_eta(eta_index);
|
||||
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);
|
||||
auto array_compute = std::unique_ptr<ElectrodeMatrix>(new ElectrodeMatrix(lmp, igroup, eta));
|
||||
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);
|
||||
} // write_mat before proceeding
|
||||
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);
|
||||
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 j = 0; j < nlocalele; j++) q_local[j] += sd_vectors[g][list_iele[j]] * group_psi[g];
|
||||
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)
|
||||
{
|
||||
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)
|
||||
{
|
||||
if (symm) {
|
||||
if (symm || qtotal_var_style != VarStyle::UNSET) {
|
||||
double sum = 0.;
|
||||
for (double xi : x) sum += xi;
|
||||
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()
|
||||
{
|
||||
for (int g = 0; g < num_of_groups; g++) {
|
||||
if (group_psi_var_styles[g] == VarStyle::CONST) continue;
|
||||
group_psi[g] = input->variable->compute_equal(group_psi_var_ids[g]);
|
||||
if (group_psi_var_styles[g] == VarStyle::CONST)
|
||||
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()
|
||||
{
|
||||
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
|
||||
double const qqrd2e = force->qqrd2e;
|
||||
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 *type = atom->type;
|
||||
double *q = atom->q;
|
||||
@ -1105,7 +1208,8 @@ double FixElectrodeConp::self_energy(int eflag)
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (groupbit & mask[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]];
|
||||
energy += e;
|
||||
if (eflag) {
|
||||
@ -1145,6 +1249,7 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag)
|
||||
double xtmp = x[i][0];
|
||||
double ytmp = x[i][1];
|
||||
double ztmp = x[i][2];
|
||||
double const eta_i = etaflag ? atom->dvector[eta_index][i] : eta;
|
||||
int itype = type[i];
|
||||
int *jlist = firstneigh[i];
|
||||
int jnum = numneigh[i];
|
||||
@ -1153,7 +1258,6 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag)
|
||||
int const j = jlist[jj] & NEIGHMASK;
|
||||
bool j_in_ele = groupbit & mask[j];
|
||||
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 dely = ytmp - x[j][1];
|
||||
@ -1162,6 +1266,16 @@ double FixElectrodeConp::gausscorr(int eflag, bool fflag)
|
||||
int jtype = type[j];
|
||||
|
||||
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 r = sqrt(rsq);
|
||||
double erfc_etar = 0.;
|
||||
|
||||
@ -70,7 +70,7 @@ class FixElectrodeConp : public Fix {
|
||||
|
||||
protected:
|
||||
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 pre_update(){};
|
||||
virtual void recompute_potential(std::vector<double>, std::vector<double>){};
|
||||
@ -79,6 +79,7 @@ class FixElectrodeConp : public Fix {
|
||||
virtual void compute_macro_matrices();
|
||||
std::vector<double> ele_ele_interaction(const std::vector<double> &);
|
||||
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> 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
|
||||
bool intelflag;
|
||||
inline virtual void intel_pack_buffers() {}
|
||||
double qtotal;
|
||||
std::string qtotal_var_name;
|
||||
int qtotal_var_id;
|
||||
VarStyle qtotal_var_style;
|
||||
|
||||
private:
|
||||
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 top_group; // used by ffield
|
||||
bool tfflag;
|
||||
int eta_index; // index of atom property for eta
|
||||
bool etaflag; // eta specified as atom property
|
||||
bool timer_flag;
|
||||
std::map<int, double> tf_types;
|
||||
// cg
|
||||
@ -142,6 +149,9 @@ class FixElectrodeConp : public Fix {
|
||||
std::vector<double> gather_ngroup(std::vector<double>);
|
||||
std::vector<double> gather_elevec_local(ElectrodeVector *);
|
||||
void set_charges(std::vector<double>);
|
||||
// qtotal
|
||||
double macro_capacitance_sum;
|
||||
void update_psi_qtotal();
|
||||
|
||||
// fix-specific electrode ID storage system:
|
||||
|
||||
|
||||
@ -30,7 +30,7 @@ FixElectrodeConq::FixElectrodeConq(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixElectrodeConp(lmp, narg, arg)
|
||||
{
|
||||
// copy const-style values across because update_psi will change group_psi
|
||||
group_q = group_psi;
|
||||
group_q = group_psi_const;
|
||||
|
||||
if (symm) {
|
||||
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");
|
||||
|
||||
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];
|
||||
|
||||
// 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]) -
|
||||
input->variable->compute_equal(group_psi_var_ids[0]);
|
||||
}
|
||||
|
||||
@ -438,6 +438,7 @@ void PPPMElectrode::compute(int eflag, int vflag)
|
||||
|
||||
start_compute();
|
||||
|
||||
/*
|
||||
if (compute_vector_called && last_invert_source) {
|
||||
// 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.
|
||||
@ -453,15 +454,17 @@ void PPPMElectrode::compute(int eflag, int vflag)
|
||||
density_brick[nz][ny][nx] += electrolyte_density_brick[nz][ny][nx];
|
||||
}
|
||||
} else {
|
||||
make_rho();
|
||||
*/
|
||||
particle_map();
|
||||
make_rho();
|
||||
|
||||
// all procs communicate density values from their ghost cells
|
||||
// to fully sum contribution in their 3d bricks
|
||||
// remap from 3d decomposition to FFT decomposition
|
||||
// all procs communicate density values from their ghost cells
|
||||
// to fully sum contribution in their 3d bricks
|
||||
// remap from 3d decomposition to FFT decomposition
|
||||
|
||||
gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2,
|
||||
MPI_FFT_SCALAR);
|
||||
}
|
||||
gc->reverse_comm(Grid3d::KSPACE, this, REVERSE_RHO, 1, sizeof(FFT_SCALAR), gc_buf1, gc_buf2,
|
||||
MPI_FFT_SCALAR);
|
||||
//}
|
||||
|
||||
brick2fft();
|
||||
|
||||
@ -584,6 +587,7 @@ void PPPMElectrode::compute_vector(double *vec, int sensor_grpbit, int source_gr
|
||||
// electrolyte density (without writing an additional function)
|
||||
FFT_SCALAR ***density_brick_real = density_brick;
|
||||
FFT_SCALAR *density_fft_real = density_fft;
|
||||
particle_map();
|
||||
make_rho_in_brick(source_grpbit, electrolyte_density_brick, invert_source);
|
||||
density_brick = electrolyte_density_brick;
|
||||
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)
|
||||
double *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++) {
|
||||
work2[n++] = greensfn[i];
|
||||
work2[n++] = ZEROF;
|
||||
@ -862,7 +867,7 @@ void PPPMElectrode::two_step_multiplication(bigint *imat, double *greens_real, d
|
||||
|
||||
double **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
|
||||
int r = abs(x);
|
||||
@ -981,17 +986,18 @@ void PPPMElectrode::allocate()
|
||||
// returns local owned and ghost grid bounds
|
||||
// setup communication patterns and buffers
|
||||
|
||||
gc = new Grid3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
|
||||
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
|
||||
nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out);
|
||||
gc = new Grid3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_in, nxhi_in, nylo_in, nyhi_in,
|
||||
nzlo_in, nzhi_in, 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;
|
||||
else npergrid = 3;
|
||||
if (differentiation_flag)
|
||||
npergrid = 1;
|
||||
else
|
||||
npergrid = 3;
|
||||
|
||||
memory->create(gc_buf1,npergrid*ngc_buf1,"pppm:gc_buf1");
|
||||
memory->create(gc_buf2,npergrid*ngc_buf2,"pppm:gc_buf2");
|
||||
memory->create(gc_buf1, npergrid * ngc_buf1, "pppm:gc_buf1");
|
||||
memory->create(gc_buf2, npergrid * ngc_buf2, "pppm:gc_buf2");
|
||||
|
||||
// tally local grid sizes
|
||||
// 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_both = greater of nfft and nfft_brick
|
||||
|
||||
ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
|
||||
(nzhi_out-nzlo_out+1);
|
||||
ngrid = (nxhi_out - nxlo_out + 1) * (nyhi_out - nylo_out + 1) * (nzhi_out - nzlo_out + 1);
|
||||
|
||||
nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) *
|
||||
(nzhi_in-nzlo_in+1);
|
||||
nfft_brick = (nxhi_in - nxlo_in + 1) * (nyhi_in - nylo_in + 1) * (nzhi_in - nzlo_in + 1);
|
||||
|
||||
nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) *
|
||||
(nzhi_fft-nzlo_fft+1);
|
||||
nfft = (nxhi_fft - nxlo_fft + 1) * (nyhi_fft - nylo_fft + 1) * (nzhi_fft - nzlo_fft + 1);
|
||||
|
||||
nfft_both = MAX(nfft,nfft_brick);
|
||||
nfft_both = MAX(nfft, nfft_brick);
|
||||
|
||||
// allocate distributed grid data
|
||||
|
||||
memory->create3d_offset(density_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
||||
nxlo_out,nxhi_out,"pppm:density_brick");
|
||||
memory->create3d_offset(density_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||
"pppm:density_brick");
|
||||
|
||||
memory->create(density_fft,nfft_both,"pppm:density_fft");
|
||||
memory->create(greensfn,nfft_both,"pppm:greensfn");
|
||||
memory->create(work1,2*nfft_both,"pppm:work1");
|
||||
memory->create(work2,2*nfft_both,"pppm:work2");
|
||||
memory->create(vg,nfft_both,6,"pppm:vg");
|
||||
memory->create(density_fft, nfft_both, "pppm:density_fft");
|
||||
memory->create(greensfn, nfft_both, "pppm:greensfn");
|
||||
memory->create(work1, 2 * nfft_both, "pppm:work1");
|
||||
memory->create(work2, 2 * nfft_both, "pppm:work2");
|
||||
memory->create(vg, nfft_both, 6, "pppm:vg");
|
||||
|
||||
if (triclinic == 0) {
|
||||
memory->create1d_offset(fkx,nxlo_fft,nxhi_fft,"pppm:fkx");
|
||||
memory->create1d_offset(fky,nylo_fft,nyhi_fft,"pppm:fky");
|
||||
memory->create1d_offset(fkz,nzlo_fft,nzhi_fft,"pppm:fkz");
|
||||
memory->create1d_offset(fkx, nxlo_fft, nxhi_fft, "pppm:fkx");
|
||||
memory->create1d_offset(fky, nylo_fft, nyhi_fft, "pppm:fky");
|
||||
memory->create1d_offset(fkz, nzlo_fft, nzhi_fft, "pppm:fkz");
|
||||
} else {
|
||||
memory->create(fkx,nfft_both,"pppm:fkx");
|
||||
memory->create(fky,nfft_both,"pppm:fky");
|
||||
memory->create(fkz,nfft_both,"pppm:fkz");
|
||||
memory->create(fkx, nfft_both, "pppm:fkx");
|
||||
memory->create(fky, nfft_both, "pppm:fky");
|
||||
memory->create(fkz, nfft_both, "pppm:fkz");
|
||||
}
|
||||
|
||||
if (differentiation_flag == 1) {
|
||||
memory->create3d_offset(u_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
||||
nxlo_out,nxhi_out,"pppm:u_brick");
|
||||
memory->create3d_offset(u_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||
"pppm:u_brick");
|
||||
|
||||
memory->create(sf_precoeff1,nfft_both,"pppm:sf_precoeff1");
|
||||
memory->create(sf_precoeff2,nfft_both,"pppm:sf_precoeff2");
|
||||
memory->create(sf_precoeff3,nfft_both,"pppm:sf_precoeff3");
|
||||
memory->create(sf_precoeff4,nfft_both,"pppm:sf_precoeff4");
|
||||
memory->create(sf_precoeff5,nfft_both,"pppm:sf_precoeff5");
|
||||
memory->create(sf_precoeff6,nfft_both,"pppm:sf_precoeff6");
|
||||
memory->create(sf_precoeff1, nfft_both, "pppm:sf_precoeff1");
|
||||
memory->create(sf_precoeff2, nfft_both, "pppm:sf_precoeff2");
|
||||
memory->create(sf_precoeff3, nfft_both, "pppm:sf_precoeff3");
|
||||
memory->create(sf_precoeff4, nfft_both, "pppm:sf_precoeff4");
|
||||
memory->create(sf_precoeff5, nfft_both, "pppm:sf_precoeff5");
|
||||
memory->create(sf_precoeff6, nfft_both, "pppm:sf_precoeff6");
|
||||
|
||||
} else {
|
||||
memory->create3d_offset(vdx_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
||||
nxlo_out,nxhi_out,"pppm:vdx_brick");
|
||||
memory->create3d_offset(vdy_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
||||
nxlo_out,nxhi_out,"pppm:vdy_brick");
|
||||
memory->create3d_offset(vdz_brick,nzlo_out,nzhi_out,nylo_out,nyhi_out,
|
||||
nxlo_out,nxhi_out,"pppm:vdz_brick");
|
||||
memory->create3d_offset(vdx_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||
"pppm:vdx_brick");
|
||||
memory->create3d_offset(vdy_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||
"pppm:vdy_brick");
|
||||
memory->create3d_offset(vdz_brick, nzlo_out, nzhi_out, nylo_out, nyhi_out, nxlo_out, nxhi_out,
|
||||
"pppm:vdz_brick");
|
||||
}
|
||||
|
||||
// summation coeffs
|
||||
|
||||
order_allocated = order;
|
||||
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(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(drho_coeff,order,(1-order)/2,order/2,
|
||||
"pppm:drho_coeff");
|
||||
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(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(drho_coeff, order, (1 - order) / 2, order / 2, "pppm:drho_coeff");
|
||||
|
||||
// create 2 FFTs and a Remap
|
||||
// 1st FFT keeps data in FFT decomposition
|
||||
@ -1069,20 +1071,17 @@ void PPPMElectrode::allocate()
|
||||
|
||||
int tmp;
|
||||
|
||||
fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
|
||||
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);
|
||||
fft1 = new FFT3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, 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);
|
||||
|
||||
fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
|
||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
||||
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
|
||||
0,0,&tmp,collective_flag);
|
||||
fft2 = new FFT3d(lmp, world, nx_pppm, ny_pppm, nz_pppm, nxlo_fft, nxhi_fft, nylo_fft, nyhi_fft,
|
||||
nzlo_fft, nzhi_fft, nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, 0, 0,
|
||||
&tmp, collective_flag);
|
||||
|
||||
remap = new Remap(lmp,world,
|
||||
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
|
||||
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
|
||||
1,0,0,FFT_PRECISION,collective_flag);
|
||||
remap = new Remap(lmp, world, nxlo_in, nxhi_in, nylo_in, nyhi_in, nzlo_in, nzhi_in, nxlo_fft,
|
||||
nxhi_fft, nylo_fft, nyhi_fft, nzlo_fft, nzhi_fft, 1, 0, 0, FFT_PRECISION,
|
||||
collective_flag);
|
||||
|
||||
// ELECTRODE specific allocations
|
||||
|
||||
|
||||
@ -22,3 +22,4 @@ angle_coeff *
|
||||
|
||||
group bot type 1
|
||||
group top type 2
|
||||
group ele type 1 2
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
---
|
||||
lammps_version: 23 Jun 2022
|
||||
date_generated: Wed Sep 21 13:52:53 2022
|
||||
lammps_version: 7 Feb 2024
|
||||
date_generated: Mon Mar 4 09:44:30 2024
|
||||
epsilon: 1e-12
|
||||
skip_tests: gpu kokkos_omp omp
|
||||
prerequisites: ! |
|
||||
@ -16,6 +16,7 @@ post_commands: ! |
|
||||
kspace_modify gewald 0.23118
|
||||
kspace_modify slab ew2d
|
||||
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
|
||||
pair_style: coul/long 15.0
|
||||
pair_coeff: ! |
|
||||
@ -27,97 +28,97 @@ init_coul: 2.215589572896434
|
||||
init_stress: ! |2-
|
||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
init_forces: ! |2
|
||||
1 2.0780648532795694e-04 1.9949672015209204e-03 3.1005914149473996e+00
|
||||
2 -1.6777235182686288e-02 2.1481432256290419e-03 3.0881659196467988e+00
|
||||
3 6.0082164895554737e-04 5.1573260226633801e-03 3.1029192412328555e+00
|
||||
4 -1.6728974802490675e-02 6.1174723156886242e-03 3.0909324782862346e+00
|
||||
5 4.2029366155132378e-02 -2.3455526736195693e-03 -1.5659617577954634e+00
|
||||
6 5.5635790919204904e-02 -2.4542947062522369e-03 -1.5693827709331334e+00
|
||||
7 4.2014920784252008e-02 -7.5287470219125008e-04 -1.5671265392163820e+00
|
||||
8 5.5808767852333470e-02 -9.9105389808573120e-04 -1.5707104957299389e+00
|
||||
9 -5.0959878750421551e-02 -2.3630298689785601e-03 -1.5769250181497101e+00
|
||||
10 -3.3526564930579039e-02 -2.3802275431282884e-03 -1.5617801011657175e+00
|
||||
11 -5.1236396351794389e-02 -4.9531100598979201e-04 -1.5779995894034005e+00
|
||||
12 -3.3740693032952060e-02 -1.0210406243572182e-03 -1.5630986537874150e+00
|
||||
13 -1.1437102611353016e-03 -4.6454866413029015e-05 5.4282837980149448e-03
|
||||
14 2.3914999373115431e-03 -1.6478680244651469e-04 2.9802178734319239e-02
|
||||
15 3.9287193302652786e-05 -2.5715673267285659e-05 2.8944525105129479e-03
|
||||
16 2.0458480716482328e-03 -1.2119161321908735e-04 3.3689550843809452e-02
|
||||
17 -2.7146073277767471e-03 -8.2376243258224663e-04 2.6564130941474612e-02
|
||||
18 1.3669692885198135e-03 -4.2357196145489820e-04 3.2396141113926739e-02
|
||||
19 3.0143371860819995e-04 -8.6218593339583785e-04 2.6284521141350669e-02
|
||||
20 1.1542435168435056e-03 -2.7252318260838826e-04 3.4237916528138110e-02
|
||||
21 -1.2350056952573553e-03 4.8655691135364269e-04 5.9284283442393631e-03
|
||||
22 2.3656743884722890e-03 9.6575340844312705e-04 2.9811074931784823e-02
|
||||
23 4.6754986244969657e-05 3.0149464050350903e-04 3.4630785686112129e-03
|
||||
24 2.0301227080749633e-03 6.3879578068684812e-04 3.3653437189053413e-02
|
||||
25 -2.3656211013513076e-03 -8.0454594828768334e-04 2.8476980555362911e-02
|
||||
26 1.1566723797447039e-03 -3.9614599888570504e-04 3.2873323713155905e-02
|
||||
27 2.8784994028036400e-04 -8.3661697184444898e-04 2.8317655886021253e-02
|
||||
28 9.3882364605486020e-04 -2.3327601777843495e-04 3.4334676606415648e-02
|
||||
29 -4.7969977052124917e-04 -1.2933334305373028e-04 -1.2336987392568071e-02
|
||||
30 6.4733118786851766e-05 -1.3190918849005797e-04 -1.2737933567178844e-02
|
||||
31 2.4269094157913586e-04 -1.3093943526788584e-04 -1.2136133260085013e-02
|
||||
32 1.7452552740941527e-04 -1.1792779046242341e-04 -1.4181538324619835e-02
|
||||
33 -3.8366266481516803e-04 -7.1061854758754556e-05 -1.3699106365426135e-02
|
||||
34 2.8849004082563746e-05 -5.7838605310673531e-05 -1.3764181266896890e-02
|
||||
35 2.2648059665862587e-04 -7.2851385190891320e-05 -1.3537361892926607e-02
|
||||
36 1.2929221129083645e-04 -4.2862960950045859e-05 -1.4926105930886896e-02
|
||||
37 -4.7698025941707008e-04 2.9971529466656788e-04 -1.2393604822896313e-02
|
||||
38 6.4231095731188766e-05 2.7548977518460050e-04 -1.2789498345723021e-02
|
||||
39 2.4169204779864826e-04 3.0552093685810269e-04 -1.2193908285665961e-02
|
||||
40 1.7324998349441456e-04 2.2898000918153004e-04 -1.4225267020837207e-02
|
||||
41 -3.4345772150395188e-04 -9.8012060153887415e-05 -1.4482722052972283e-02
|
||||
42 2.0345466940577010e-05 -8.5250083485342566e-05 -1.4497101004472062e-02
|
||||
43 2.0917627239292995e-04 -1.0051271468149899e-04 -1.4335313646556430e-02
|
||||
44 1.1456796622437295e-04 -6.7553675788598551e-05 -1.5543196158604005e-02
|
||||
1 2.0780648532797705e-04 1.9949672015210172e-03 3.1005914149473988e+00
|
||||
2 -1.6777235182686239e-02 2.1481432256291962e-03 3.0881659196467979e+00
|
||||
3 6.0082164895566240e-04 5.1573260226632518e-03 3.1029192412328550e+00
|
||||
4 -1.6728974802490665e-02 6.1174723156885227e-03 3.0909324782862333e+00
|
||||
5 4.2029366155132364e-02 -2.3455526736195940e-03 -1.5659617577954636e+00
|
||||
6 5.5635790919204904e-02 -2.4542947062522933e-03 -1.5693827709331336e+00
|
||||
7 4.2014920784251980e-02 -7.5287470219118655e-04 -1.5671265392163822e+00
|
||||
8 5.5808767852333491e-02 -9.9105389808568046e-04 -1.5707104957299391e+00
|
||||
9 -5.0959878750421538e-02 -2.3630298689785965e-03 -1.5769250181497101e+00
|
||||
10 -3.3526564930579081e-02 -2.3802275431283552e-03 -1.5617801011657175e+00
|
||||
11 -5.1236396351794437e-02 -4.9531100598972577e-04 -1.5779995894034005e+00
|
||||
12 -3.3740693032952088e-02 -1.0210406243571744e-03 -1.5630986537874152e+00
|
||||
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
30 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
31 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
32 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
33 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
34 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
35 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
36 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
37 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
38 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
39 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
40 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
41 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
42 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
43 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
44 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
run_vdwl: 0
|
||||
run_coul: 6.662694629990089
|
||||
run_coul: 6.662694556930397
|
||||
run_stress: ! |2-
|
||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
run_forces: ! |2
|
||||
1 2.4590612609445102e-04 1.9614041218568861e-03 3.0874291949281147e+00
|
||||
2 -1.6646393233505193e-02 2.1136941574790400e-03 3.0751132981100078e+00
|
||||
3 6.3535217476586373e-04 5.1012487117746350e-03 3.0897301317927290e+00
|
||||
4 -1.6598677148313409e-02 6.0535154567108685e-03 3.0778495346381409e+00
|
||||
5 4.2257888534896988e-02 -2.3028533365965051e-03 -1.5593100596807521e+00
|
||||
6 5.5690508027606708e-02 -2.4104721624763235e-03 -1.5626897542440843e+00
|
||||
7 4.2243973130370149e-02 -7.6153220413259775e-04 -1.5604618260035832e+00
|
||||
8 5.5862703939049158e-02 -9.9825803703216718e-04 -1.5640031014325448e+00
|
||||
9 -5.1059409954744304e-02 -2.3195553026588347e-03 -1.5701677851024036e+00
|
||||
10 -3.3824298857146967e-02 -2.3375522139358631e-03 -1.5551647619109401e+00
|
||||
11 -5.1334079184640377e-02 -5.0583705005136689e-04 -1.5712298444761112e+00
|
||||
12 -3.4037363466305925e-02 -1.0275978089057873e-03 -1.5564691026885336e+00
|
||||
13 -1.1767076011504501e-03 -4.7681963272732406e-05 5.6177800544716262e-03
|
||||
14 2.3826294437743331e-03 -1.6349140124449633e-04 2.9836275824428962e-02
|
||||
15 4.1635367214843796e-05 -2.7287283914685102e-05 3.0967012748694773e-03
|
||||
16 2.0334138778396313e-03 -1.1986039772787527e-04 3.3679727731055195e-02
|
||||
17 -2.7026084826568797e-03 -8.1815079485725360e-04 2.6574868248546435e-02
|
||||
18 1.3603406762441243e-03 -4.1902595052936860e-04 3.2373613783594497e-02
|
||||
19 2.9940467686436986e-04 -8.5646794759970863e-04 2.6296909514905095e-02
|
||||
20 1.1469475577225402e-03 -2.6907093945665336e-04 3.4197589258157073e-02
|
||||
21 -1.2662578686531134e-03 4.9770031968890231e-04 6.1141650873547037e-03
|
||||
22 2.3568409810395020e-03 9.5671841592085381e-04 2.9844352492872490e-02
|
||||
23 4.8965507374742117e-05 3.1616579858329929e-04 3.6613180489820005e-03
|
||||
24 2.0177821554069170e-03 6.3083810187911310e-04 3.3643353017422439e-02
|
||||
25 -2.3537455003017457e-03 -7.9846295760147956e-04 2.8468250829639500e-02
|
||||
26 1.1507655048236000e-03 -3.9159985067612060e-04 3.2839870487003708e-02
|
||||
27 2.8582562554448814e-04 -8.3038492818152999e-04 2.8309777443009273e-02
|
||||
28 9.3274285761092680e-04 -2.2997823984283208e-04 3.4287630335266286e-02
|
||||
29 -4.7502414048888327e-04 -1.2847214455389489e-04 -1.2453998829891042e-02
|
||||
30 6.3675154563755000e-05 -1.3104204562344653e-04 -1.2848240218511071e-02
|
||||
31 2.4068203429808906e-04 -1.3007692195448562e-04 -1.2254443488117142e-02
|
||||
32 1.7286880375665112e-04 -1.1713944254614034e-04 -1.4279748536149278e-02
|
||||
33 -3.7975304094097439e-04 -7.0481503989778179e-05 -1.3805675914786045e-02
|
||||
34 2.8172580422574018e-05 -5.7414812953860394e-05 -1.3867744309035916e-02
|
||||
35 2.2448042926710853e-04 -7.2258368796568220e-05 -1.3645037267085249e-02
|
||||
36 1.2804302797390986e-04 -4.2547023166907131e-05 -1.5019384166440140e-02
|
||||
37 -4.7231656130619122e-04 2.9759414220405656e-04 -1.2510308090752414e-02
|
||||
38 6.3181133759042352e-05 2.7366531591578288e-04 -1.2899551129187765e-02
|
||||
39 2.3968383978790597e-04 3.0338116638639894e-04 -1.2311919409216509e-02
|
||||
40 1.7159804905743131e-04 2.2744508340904917e-04 -1.4323246783684936e-02
|
||||
41 -3.3986046011853923e-04 -9.7274166717457145e-05 -1.4583591616566860e-02
|
||||
42 1.9775995840422978e-05 -8.4675117269364898e-05 -1.4595729099929700e-02
|
||||
43 2.0725822207231137e-04 -9.9764702521265135e-05 -1.4437236974797743e-02
|
||||
44 1.1345006523014360e-04 -6.7103771021504086e-05 -1.5632251527466189e-02
|
||||
1 2.4590683616588566e-04 1.9614031577864796e-03 3.0874292323214036e+00
|
||||
2 -1.6646391056109287e-02 2.1136931488459688e-03 3.0751133344119794e+00
|
||||
3 6.3535284261976926e-04 5.1012486499620825e-03 3.0897301693141319e+00
|
||||
4 -1.6598674977089559e-02 6.0535154273402107e-03 3.0778495712965124e+00
|
||||
5 4.2257890248609438e-02 -2.3028528771736243e-03 -1.5593100743454236e+00
|
||||
6 5.5690508840794850e-02 -2.4104716736066006e-03 -1.5626897684026868e+00
|
||||
7 4.2243974848895645e-02 -7.6153214117129057e-04 -1.5604618407191602e+00
|
||||
8 5.5862704771247280e-02 -9.9825804058299890e-04 -1.5640031157582626e+00
|
||||
9 -5.1059412079591346e-02 -2.3195548367148894e-03 -1.5701677996288432e+00
|
||||
10 -3.3824301875619085e-02 -2.3375517362837230e-03 -1.5551647759943836e+00
|
||||
11 -5.1334081278836916e-02 -5.0583707575582921e-04 -1.5712298590599834e+00
|
||||
12 -3.4037366496628307e-02 -1.0275977984217173e-03 -1.5564691169384559e+00
|
||||
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
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|
||||
...
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
---
|
||||
lammps_version: 23 Jun 2022
|
||||
date_generated: Wed Sep 21 13:52:39 2022
|
||||
lammps_version: 7 Feb 2024
|
||||
date_generated: Mon Mar 4 09:44:31 2024
|
||||
epsilon: 3e-12
|
||||
skip_tests: gpu kokkos_omp omp
|
||||
prerequisites: ! |
|
||||
@ -16,6 +16,7 @@ post_commands: ! |
|
||||
kspace_modify gewald 0.23118
|
||||
kspace_modify slab 3.0
|
||||
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
|
||||
pair_style: coul/long 15.0
|
||||
pair_coeff: ! |
|
||||
@ -23,101 +24,101 @@ pair_coeff: ! |
|
||||
extract: ! ""
|
||||
natoms: 44
|
||||
init_vdwl: 0
|
||||
init_coul: 2.2156402256727614
|
||||
init_coul: 2.215640225672775
|
||||
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|
||||
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||||
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||||
run_vdwl: 0
|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
34 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
35 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
36 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
37 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
38 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
39 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
40 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
41 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
42 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
43 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
44 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
...
|
||||
|
||||
Reference in New Issue
Block a user