implement compute_array
This commit is contained in:
srtee
@ -130,48 +130,49 @@ file, for code developers to track optimization.
|
||||
|
||||
fix_modify ID timer on/off
|
||||
|
||||
The *fix_modify set* options allow calculated quantities to be accessed via
|
||||
internal variables. Currently four types of quantities can be accessed:
|
||||
----------
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
These fixes compute a global array which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The array has *N* rows and *2N+2*
|
||||
columns, where *N* is the number of electrode groups managed by the fix. For the
|
||||
*I*-th row of the array, the elements are:
|
||||
|
||||
fix-modify ID set v group-ID variablename
|
||||
fix-modify ID set qsb group-ID variablename
|
||||
fix-modify ID set mc group-ID1 group-ID2 variablename
|
||||
fix-modify ID set me group-ID1 group-ID2 variablename
|
||||
* array[I][1] = potential instantaneously applied to group *I*
|
||||
* array[I][1] = total charge that group *I* would have had *if it were at 0 V
|
||||
applied potential*
|
||||
* array[I][2 to *N* + 1] = the *N* entries of the *I*-th row of the electrode
|
||||
capacitance matrix (definition follows)
|
||||
* array[I][*N* + 2 to *2N* + 1] = the *N* entries of the *I*-th row of the electrode
|
||||
elastance matrix (the inverse of the electrode capacitance matrix)
|
||||
|
||||
One use case is to output the potential that is internally calculated and
|
||||
applied to each electrode group by *fix electrode/conq* or *fix electrode/thermo*.
|
||||
For that case the *v* option makes *fix electrode* update the variable
|
||||
*variablename* with the potential applied to group *group-ID*, where *group-ID*
|
||||
must be a group whose charges are updated by *fix electrode* and *variablename*
|
||||
must be an internal-style variable:
|
||||
The first column is handy for *fix electrode/conq* and *fix
|
||||
electrode/thermo* simulations, to output the potentials dynamically calculated and
|
||||
imposed by the fix (see following formula). The potential is in units of electric field times
|
||||
distance, which gives volts for most (but not all) :doc:`units <units>` settings.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix conq bot electrode/conq -1.0 1.979 couple top 1.0
|
||||
variable vbot internal 0.0
|
||||
fix_modify conq set v bot vbot
|
||||
|
||||
The *qsb* option similarly outputs the total updated charge of the group if its
|
||||
potential were 0.0V. The *mc* option requires two *group-IDs*, and outputs the
|
||||
entry \{*group-ID1*, *group-ID2*\} of the (symmetric) *macro-capacitance* matrix
|
||||
(MC) which relates the electrodes' applied potentials (V), total charges (Q), and
|
||||
total charges at 0.0 V (Qsb):
|
||||
The :math:`N \times N` electrode capacitance matrix, denoted :math:`\mathbf{C}`
|
||||
in the following equation, summarizes how the total charge induced on each electrode
|
||||
(:math:`\mathbf{Q}` as an *N*-vector) is related to the potential on each
|
||||
electrode, :math:`\mathbf{V}`, and the charge-at-0V :math:`\mathbf{Q}_{0V}`
|
||||
(which is influenced by the local electrolyte structure):
|
||||
|
||||
.. math::
|
||||
|
||||
\mathbf{Q} = \mathbf{Q}_{SB} + \mathbf{MC} \cdot \mathbf{V}
|
||||
\mathbf{Q} = \mathbf{Q}_{0V} + \mathbf{C} \cdot \mathbf{V}
|
||||
|
||||
Lastly, the *me* option also requires two *group-IDs* and outputs the entry
|
||||
\{*group-ID1*, *group-ID2*\} of the *macro-elastance* matrix, which is the
|
||||
inverse of the macro-capacitance matrix. (As the names denote, the
|
||||
macro-capacitance matrix gives electrode charges from potentials, and the
|
||||
macro-elastance matrix gives electrode potentials from charges).
|
||||
The charge-at-0V, electrode capacitance and elastance matrices are internally used to
|
||||
calculate the potentials required to induce the specified total electrode charges
|
||||
in *fix electrode/conq* and *fix electrode/thermo*. With the *symm on* option,
|
||||
the electrode capacitance matrix would be singular, and thus its last row is
|
||||
replaced with *N* copies of its top-left entry (:math:`\mathbf{C}_{11}`) for
|
||||
invertibility.
|
||||
|
||||
.. warning::
|
||||
----------
|
||||
|
||||
Positions of electrode particles have to be immobilized at all times.
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
Positions of electrode particles have to be immobilized at all times.
|
||||
|
||||
The parallelization for the fix works best if electrode atoms are evenly
|
||||
distributed across processors. For a system with two electrodes at the bottom
|
||||
|
||||
@ -7,12 +7,6 @@ kspace_modify slab 3.0
|
||||
|
||||
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
|
||||
|
||||
# ask fix conq to output electrode potentials to internal variables
|
||||
variable vbot internal 0.0
|
||||
variable vtop internal 0.0
|
||||
fix_modify conq set v bot vbot
|
||||
fix_modify conq set v top vtop
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1][1] f_conq[2][1]
|
||||
run 500
|
||||
|
||||
@ -7,28 +7,14 @@ kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5
|
||||
|
||||
# get the four entries of electrode elastance matrix
|
||||
variable me00 internal 0.0
|
||||
variable me01 internal 0.0
|
||||
variable me10 internal 0.0
|
||||
variable me11 internal 0.0
|
||||
fix_modify conp set me bot bot me00
|
||||
fix_modify conp set me bot top me01
|
||||
fix_modify conp set me top bot me10
|
||||
fix_modify conp set me top top me11
|
||||
|
||||
# get the 0V charges (qsb), and excess charge required to reach preset total charges
|
||||
variable qsb_bot internal 0.0
|
||||
variable qsb_top internal 0.0
|
||||
fix_modify conp set qsb bot qsb_bot
|
||||
fix_modify conp set qsb top qsb_top
|
||||
variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge
|
||||
variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge
|
||||
variable qex_bot equal -1.0-f_conp[1][2] # difference between desired and 0V charge
|
||||
variable qex_top equal 1.0-f_conp[2][2] # difference between desired and 0V charge
|
||||
|
||||
# calculate imposed potential as elastance * excess charge
|
||||
# note: fix will wait until the run setup to look for its potential variables
|
||||
variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top
|
||||
variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top
|
||||
# which is why we can define variable names *after* fix conp without error
|
||||
variable vbot equal f_conp[1][5]*v_qex_bot+f_conp[1][6]*v_qex_top
|
||||
variable vtop equal f_conp[2][5]*v_qex_bot+f_conp[2][6]*v_qex_top
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
|
||||
@ -67,14 +67,8 @@ kspace_modify slab 3.0
|
||||
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
|
||||
832 atoms in group conp_group
|
||||
|
||||
# ask fix conq to output electrode potentials to internal variables
|
||||
variable vbot internal 0.0
|
||||
variable vtop internal 0.0
|
||||
fix_modify conq set v bot vbot
|
||||
fix_modify conq set v top vtop
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1][1] f_conq[2][1]
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
@ -109,7 +103,7 @@ Neighbor list info ...
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1][1] f_conq[2][1]
|
||||
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344
|
||||
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514
|
||||
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787
|
||||
@ -121,22 +115,22 @@ Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
|
||||
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
|
||||
Loop time of 48.9361 on 1 procs for 500 steps with 3776 atoms
|
||||
Loop time of 42.3981 on 1 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 0.883 ns/day, 27.187 hours/ns, 10.217 timesteps/s
|
||||
393.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 1.019 ns/day, 23.555 hours/ns, 11.793 timesteps/s
|
||||
393.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 17.652 | 17.652 | 17.652 | 0.0 | 36.07
|
||||
Bond | 0.0010418 | 0.0010418 | 0.0010418 | 0.0 | 0.00
|
||||
Kspace | 16.566 | 16.566 | 16.566 | 0.0 | 33.85
|
||||
Neigh | 0.21584 | 0.21584 | 0.21584 | 0.0 | 0.44
|
||||
Comm | 0.04167 | 0.04167 | 0.04167 | 0.0 | 0.09
|
||||
Output | 0.0014585 | 0.0014585 | 0.0014585 | 0.0 | 0.00
|
||||
Modify | 14.445 | 14.445 | 14.445 | 0.0 | 29.52
|
||||
Other | | 0.0134 | | | 0.03
|
||||
Pair | 15.337 | 15.337 | 15.337 | 0.0 | 36.17
|
||||
Bond | 0.00098464 | 0.00098464 | 0.00098464 | 0.0 | 0.00
|
||||
Kspace | 16.11 | 16.11 | 16.11 | 0.0 | 38.00
|
||||
Neigh | 0.19136 | 0.19136 | 0.19136 | 0.0 | 0.45
|
||||
Comm | 0.039778 | 0.039778 | 0.039778 | 0.0 | 0.09
|
||||
Output | 0.0015193 | 0.0015193 | 0.0015193 | 0.0 | 0.00
|
||||
Modify | 10.705 | 10.705 | 10.705 | 0.0 | 25.25
|
||||
Other | | 0.01253 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -150,4 +144,4 @@ Ave neighs/atom = 456.98835
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:43
|
||||
Total wall time: 0:01:34
|
||||
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.020 seconds
|
||||
read_data CPU = 0.018 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
@ -68,14 +68,8 @@ kspace_modify slab 3.0
|
||||
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
|
||||
832 atoms in group conp_group
|
||||
|
||||
# ask fix conq to output electrode potentials to internal variables
|
||||
variable vbot internal 0.0
|
||||
variable vtop internal 0.0
|
||||
fix_modify conq set v bot vbot
|
||||
fix_modify conq set v top vtop
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1][1] f_conq[2][1]
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
@ -110,7 +104,7 @@ Neighbor list info ...
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1][1] f_conq[2][1]
|
||||
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344
|
||||
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514
|
||||
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787
|
||||
@ -122,22 +116,22 @@ Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
|
||||
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
|
||||
Loop time of 28.8336 on 4 procs for 500 steps with 3776 atoms
|
||||
Loop time of 23.02 on 4 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 1.498 ns/day, 16.019 hours/ns, 17.341 timesteps/s
|
||||
94.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 1.877 ns/day, 12.789 hours/ns, 21.720 timesteps/s
|
||||
93.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.7721 | 5.9353 | 6.144 | 6.0 | 20.58
|
||||
Bond | 0.00057855 | 0.00067043 | 0.00074793 | 0.0 | 0.00
|
||||
Kspace | 13.485 | 13.694 | 13.857 | 4.0 | 47.49
|
||||
Neigh | 0.092021 | 0.092044 | 0.092068 | 0.0 | 0.32
|
||||
Comm | 0.11486 | 0.11638 | 0.11801 | 0.4 | 0.40
|
||||
Output | 0.00090452 | 0.001109 | 0.0017097 | 1.0 | 0.00
|
||||
Modify | 8.974 | 8.9761 | 8.978 | 0.1 | 31.13
|
||||
Other | | 0.01837 | | | 0.06
|
||||
Pair | 4.0178 | 4.1947 | 4.3354 | 6.8 | 18.22
|
||||
Bond | 0.00061117 | 0.00068637 | 0.00072249 | 0.0 | 0.00
|
||||
Kspace | 11.853 | 11.994 | 12.171 | 4.0 | 52.10
|
||||
Neigh | 0.060425 | 0.060489 | 0.06052 | 0.0 | 0.26
|
||||
Comm | 0.091334 | 0.092251 | 0.093191 | 0.3 | 0.40
|
||||
Output | 0.00067425 | 0.00089541 | 0.0014804 | 0.0 | 0.00
|
||||
Modify | 6.6612 | 6.662 | 6.6627 | 0.0 | 28.94
|
||||
Other | | 0.01505 | | | 0.07
|
||||
|
||||
Nlocal: 944 ave 948 max 940 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
@ -151,4 +145,4 @@ Ave neighs/atom = 456.98835
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:51
|
||||
Total wall time: 0:00:44
|
||||
@ -38,7 +38,7 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.031 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
@ -67,28 +67,14 @@ kspace_modify slab 3.0
|
||||
fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5
|
||||
832 atoms in group conp_group
|
||||
|
||||
# get the four entries of electrode elastance matrix
|
||||
variable me00 internal 0.0
|
||||
variable me01 internal 0.0
|
||||
variable me10 internal 0.0
|
||||
variable me11 internal 0.0
|
||||
fix_modify conp set me bot bot me00
|
||||
fix_modify conp set me bot top me01
|
||||
fix_modify conp set me top bot me10
|
||||
fix_modify conp set me top top me11
|
||||
|
||||
# get the 0V charges (qsb), and excess charge required to reach preset total charges
|
||||
variable qsb_bot internal 0.0
|
||||
variable qsb_top internal 0.0
|
||||
fix_modify conp set qsb bot qsb_bot
|
||||
fix_modify conp set qsb top qsb_top
|
||||
variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge
|
||||
variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge
|
||||
variable qex_bot equal -1.0-f_conp[1][2] # difference between desired and 0V charge
|
||||
variable qex_top equal 1.0-f_conp[2][2] # difference between desired and 0V charge
|
||||
|
||||
# calculate imposed potential as elastance * excess charge
|
||||
# note: fix will wait until the run setup to look for its potential variables
|
||||
variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top
|
||||
variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top
|
||||
# which is why we can define variable names *after* fix conp without error
|
||||
variable vbot equal f_conp[1][5]*v_qex_bot+f_conp[1][6]*v_qex_top
|
||||
variable vtop equal f_conp[2][5]*v_qex_bot+f_conp[2][6]*v_qex_top
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
@ -138,22 +124,22 @@ Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
|
||||
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
|
||||
Loop time of 62.9692 on 1 procs for 500 steps with 3776 atoms
|
||||
Loop time of 42.7942 on 1 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 0.686 ns/day, 34.983 hours/ns, 7.940 timesteps/s
|
||||
393.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 1.009 ns/day, 23.775 hours/ns, 11.684 timesteps/s
|
||||
394.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 20.307 | 20.307 | 20.307 | 0.0 | 32.25
|
||||
Bond | 0.0020074 | 0.0020074 | 0.0020074 | 0.0 | 0.00
|
||||
Kspace | 23.562 | 23.562 | 23.562 | 0.0 | 37.42
|
||||
Neigh | 0.26149 | 0.26149 | 0.26149 | 0.0 | 0.42
|
||||
Comm | 0.059436 | 0.059436 | 0.059436 | 0.0 | 0.09
|
||||
Output | 0.0023888 | 0.0023888 | 0.0023888 | 0.0 | 0.00
|
||||
Modify | 18.756 | 18.756 | 18.756 | 0.0 | 29.79
|
||||
Other | | 0.01897 | | | 0.03
|
||||
Pair | 15.743 | 15.743 | 15.743 | 0.0 | 36.79
|
||||
Bond | 0.00097932 | 0.00097932 | 0.00097932 | 0.0 | 0.00
|
||||
Kspace | 16.028 | 16.028 | 16.028 | 0.0 | 37.45
|
||||
Neigh | 0.21147 | 0.21147 | 0.21147 | 0.0 | 0.49
|
||||
Comm | 0.040091 | 0.040091 | 0.040091 | 0.0 | 0.09
|
||||
Output | 0.001878 | 0.001878 | 0.001878 | 0.0 | 0.00
|
||||
Modify | 10.756 | 10.756 | 10.756 | 0.0 | 25.13
|
||||
Other | | 0.01243 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -167,4 +153,4 @@ Ave neighs/atom = 456.98835
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:26
|
||||
Total wall time: 0:01:35
|
||||
@ -68,28 +68,14 @@ kspace_modify slab 3.0
|
||||
fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5
|
||||
832 atoms in group conp_group
|
||||
|
||||
# get the four entries of electrode elastance matrix
|
||||
variable me00 internal 0.0
|
||||
variable me01 internal 0.0
|
||||
variable me10 internal 0.0
|
||||
variable me11 internal 0.0
|
||||
fix_modify conp set me bot bot me00
|
||||
fix_modify conp set me bot top me01
|
||||
fix_modify conp set me top bot me10
|
||||
fix_modify conp set me top top me11
|
||||
|
||||
# get the 0V charges (qsb), and excess charge required to reach preset total charges
|
||||
variable qsb_bot internal 0.0
|
||||
variable qsb_top internal 0.0
|
||||
fix_modify conp set qsb bot qsb_bot
|
||||
fix_modify conp set qsb top qsb_top
|
||||
variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge
|
||||
variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge
|
||||
variable qex_bot equal -1.0-f_conp[1][2] # difference between desired and 0V charge
|
||||
variable qex_top equal 1.0-f_conp[2][2] # difference between desired and 0V charge
|
||||
|
||||
# calculate imposed potential as elastance * excess charge
|
||||
# note: fix will wait until the run setup to look for its potential variables
|
||||
variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top
|
||||
variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top
|
||||
# which is why we can define variable names *after* fix conp without error
|
||||
variable vbot equal f_conp[1][5]*v_qex_bot+f_conp[1][6]*v_qex_top
|
||||
variable vtop equal f_conp[2][5]*v_qex_bot+f_conp[2][6]*v_qex_top
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
@ -139,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
|
||||
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
|
||||
Loop time of 33.4031 on 4 procs for 500 steps with 3776 atoms
|
||||
Loop time of 23.4395 on 4 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 1.293 ns/day, 18.557 hours/ns, 14.969 timesteps/s
|
||||
94.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 1.843 ns/day, 13.022 hours/ns, 21.331 timesteps/s
|
||||
93.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.1262 | 7.3913 | 7.611 | 6.8 | 22.13
|
||||
Bond | 0.0007191 | 0.00079089 | 0.00087005 | 0.0 | 0.00
|
||||
Kspace | 15.139 | 15.358 | 15.623 | 4.7 | 45.98
|
||||
Neigh | 0.10374 | 0.10377 | 0.10383 | 0.0 | 0.31
|
||||
Comm | 0.14245 | 0.14353 | 0.14563 | 0.3 | 0.43
|
||||
Output | 0.0012987 | 0.0015671 | 0.0022434 | 1.0 | 0.00
|
||||
Modify | 10.381 | 10.383 | 10.384 | 0.0 | 31.08
|
||||
Other | | 0.02134 | | | 0.06
|
||||
Pair | 4.1961 | 4.3786 | 4.5496 | 7.6 | 18.68
|
||||
Bond | 0.00057323 | 0.00065148 | 0.00075008 | 0.0 | 0.00
|
||||
Kspace | 11.998 | 12.168 | 12.35 | 4.6 | 51.91
|
||||
Neigh | 0.064936 | 0.064967 | 0.064998 | 0.0 | 0.28
|
||||
Comm | 0.089828 | 0.091261 | 0.092661 | 0.4 | 0.39
|
||||
Output | 0.00082362 | 0.0010221 | 0.0015517 | 1.0 | 0.00
|
||||
Modify | 6.7177 | 6.7195 | 6.7212 | 0.1 | 28.67
|
||||
Other | | 0.01535 | | | 0.07
|
||||
|
||||
Nlocal: 944 ave 948 max 940 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
@ -168,4 +154,4 @@ Ave neighs/atom = 456.98835
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:01
|
||||
Total wall time: 0:00:44
|
||||
@ -22,8 +22,8 @@
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "electrode_accel_interface.h"
|
||||
#include "electrode_matrix.h"
|
||||
#include "electrode_math.h"
|
||||
#include "electrode_matrix.h"
|
||||
#include "electrode_vector.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
@ -73,7 +73,7 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
||||
ffield = false;
|
||||
thermo_time = 0.;
|
||||
scalar_flag = 1;
|
||||
vector_flag = 1;
|
||||
array_flag = 1;
|
||||
top_group = 0;
|
||||
intelflag = false;
|
||||
tfflag = false;
|
||||
@ -222,7 +222,8 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
||||
"Cannot write elastance matrix if reading capacitance matrix "
|
||||
"from file");
|
||||
num_of_groups = static_cast<int>(groups.size());
|
||||
size_vector = num_of_groups;
|
||||
size_array_rows = num_of_groups;
|
||||
size_array_cols = 2 + 2 * num_of_groups;
|
||||
|
||||
// check groups are consistent
|
||||
int *mask = atom->mask;
|
||||
@ -260,12 +261,6 @@ FixElectrodeConp::FixElectrodeConp(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
// 0 1 2 3 return 4 if successful
|
||||
// fix_modify fxupdate set v [group] [var]
|
||||
// fix_modify fxupdate set qsb [group] [var]
|
||||
// 0 1 2 3 4 return 5 if successful
|
||||
// fix_modify fxupdate set mc [group1] [group2] [var]
|
||||
// fix_modify fxupdate set me [group1] [group2] [var]
|
||||
int FixElectrodeConp::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (strcmp(arg[0], "tf") == 0) {
|
||||
@ -306,49 +301,6 @@ int FixElectrodeConp::modify_param(int narg, char **arg)
|
||||
timer_flag = utils::logical(FLERR, arg[1], false, lmp);
|
||||
return 2;
|
||||
|
||||
} else if (strcmp(arg[0], "set") == 0) {
|
||||
if (strcmp(arg[1], "v") == 0 || strcmp(arg[1], "qsb") == 0) {
|
||||
if (narg != 4)
|
||||
error->all(FLERR,
|
||||
fmt::format("Incorrect number of arguments for fix_modify set {}", arg[1]));
|
||||
int outputgrp = groupnum_from_name(arg[2]);
|
||||
int outputvar = input->variable->find(arg[3]);
|
||||
if (outputvar < 0)
|
||||
error->all(FLERR,
|
||||
fmt::format("Variable {} for fix_modify electrode does not exist", arg[3]));
|
||||
if (!input->variable->internalstyle(outputvar))
|
||||
error->all(FLERR,
|
||||
fmt::format("Variable {} for fix_modify electrode is invalid style", arg[3]));
|
||||
if (strcmp(arg[1], "v") == 0)
|
||||
setvars_types.push_back(V);
|
||||
else
|
||||
setvars_types.push_back(QSB);
|
||||
setvars_groups.push_back(outputgrp);
|
||||
setvars_vars.push_back(outputvar);
|
||||
return 4;
|
||||
} else if (strcmp(arg[1], "mc") == 0 || strcmp(arg[1], "me") == 0) {
|
||||
if (narg != 5)
|
||||
error->all(FLERR,
|
||||
fmt::format("Incorrect number of arguments for fix_modify set {}", arg[1]));
|
||||
int outputgrpi = groupnum_from_name(arg[2]);
|
||||
int outputgrpj = groupnum_from_name(arg[3]);
|
||||
int outputgrpij = outputgrpi * num_of_groups + outputgrpj;
|
||||
int outputvar = input->variable->find(arg[4]);
|
||||
if (outputvar < 0)
|
||||
error->all(FLERR,
|
||||
fmt::format("Variable {} for fix_modify electrode does not exist", arg[4]));
|
||||
if (!input->variable->internalstyle(outputvar))
|
||||
error->all(FLERR,
|
||||
fmt::format("Variable {} for fix_modify electrode is invalid style", arg[4]));
|
||||
if (strcmp(arg[1], "mc") == 0)
|
||||
setvars_types.push_back(MC);
|
||||
else
|
||||
setvars_types.push_back(ME);
|
||||
setvars_groups.push_back(outputgrpij);
|
||||
setvars_vars.push_back(outputvar);
|
||||
return 5;
|
||||
} else
|
||||
error->all(FLERR, "Invalid set option for fix_modify electrode");
|
||||
} else
|
||||
error->all(FLERR, "Invalid argument for fix_modify electrode");
|
||||
return 0;
|
||||
@ -452,10 +404,6 @@ void FixElectrodeConp::setup_post_neighbor()
|
||||
int *mask = atom->mask;
|
||||
tagint *tag = atom->tag;
|
||||
|
||||
// setvars asserts:
|
||||
assert(setvars_groups.size() == setvars_vars.size());
|
||||
assert(setvars_groups.size() == setvars_types.size());
|
||||
|
||||
// if Thomas-Fermi, make sure all electrode atoms have parameters
|
||||
if (tfflag) {
|
||||
int unset_tf = 0;
|
||||
@ -539,8 +487,8 @@ void FixElectrodeConp::setup_post_neighbor()
|
||||
compute_macro_matrices();
|
||||
MPI_Barrier(world);
|
||||
if (timer_flag && (comm->me == 0))
|
||||
utils::logmesg(lmp,
|
||||
fmt::format("SD-vector and macro matrices time: {:.4g} s\n", MPI_Wtime() - start));
|
||||
utils::logmesg(
|
||||
lmp, fmt::format("SD-vector and macro matrices time: {:.4g} s\n", MPI_Wtime() - start));
|
||||
|
||||
// initial charges and b vector
|
||||
update_charges();
|
||||
@ -789,9 +737,7 @@ void FixElectrodeConp::update_charges()
|
||||
gather_elevec(charge_iele);
|
||||
MPI_Allreduce(MPI_IN_PLACE, &sb_charges.front(), num_of_groups, MPI_DOUBLE, MPI_SUM, world);
|
||||
|
||||
update_setvars(QSB);
|
||||
update_psi(); // use for equal-style and conq
|
||||
update_setvars(V); // push psi into 'fix_modify set' vars
|
||||
update_psi(); // use for equal-style and conq
|
||||
|
||||
for (int g = 0; g < num_of_groups; g++)
|
||||
for (int j = 0; j < ngroup; j++) { charge_iele[j] += sd_vectors[g][j] * group_psi[g]; }
|
||||
@ -820,34 +766,6 @@ void FixElectrodeConp::update_psi()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixElectrodeConp::update_setvars(int vtype)
|
||||
{
|
||||
int num_of_vars = static_cast<int>(setvars_groups.size());
|
||||
for (int v = 0; v < num_of_vars; v++) {
|
||||
if (vtype != setvars_types[v]) continue;
|
||||
switch (vtype) {
|
||||
case V:
|
||||
input->variable->internal_set(setvars_vars[v], group_psi[setvars_groups[v]]);
|
||||
break;
|
||||
case QSB:
|
||||
input->variable->internal_set(setvars_vars[v], sb_charges[setvars_groups[v]]);
|
||||
break;
|
||||
case MC: {
|
||||
int groupi = setvars_groups[v] / num_of_groups;
|
||||
int groupj = setvars_groups[v] % num_of_groups;
|
||||
input->variable->internal_set(setvars_vars[v], macro_capacitance[groupi][groupj]);
|
||||
} break;
|
||||
case ME: {
|
||||
int groupi = setvars_groups[v] / num_of_groups;
|
||||
int groupj = setvars_groups[v] % num_of_groups;
|
||||
input->variable->internal_set(setvars_vars[v], macro_elastance[groupi][groupj]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixElectrodeConp::compute_macro_matrices()
|
||||
{
|
||||
macro_capacitance =
|
||||
@ -902,9 +820,6 @@ void FixElectrodeConp::compute_macro_matrices()
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
update_setvars(MC);
|
||||
update_setvars(ME);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -915,9 +830,22 @@ double FixElectrodeConp::compute_scalar()
|
||||
}
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double FixElectrodeConp::compute_vector(int i)
|
||||
double FixElectrodeConp::compute_array(int i, int j)
|
||||
{
|
||||
return group_psi[i];
|
||||
if (i < 0 || i >= num_of_groups) error->all(FLERR, "invalid fix electrode array row reference");
|
||||
if (j < 0)
|
||||
error->all(FLERR, "invalid fix electrode array column reference");
|
||||
else if (j == 0)
|
||||
return group_psi[i];
|
||||
else if (j == 1)
|
||||
return sb_charges[i];
|
||||
else if (j <= num_of_groups + 1)
|
||||
return macro_capacitance[i][j - 2];
|
||||
else if (j <= 2 * num_of_groups + 1)
|
||||
return macro_elastance[i][j - num_of_groups - 2];
|
||||
else
|
||||
error->all(FLERR, "invalid fix electrode array column reference");
|
||||
return 0.; // avoid -Wreturn-type warning
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -46,7 +46,7 @@ class FixElectrodeConp : public Fix {
|
||||
void pre_force(int) override;
|
||||
void pre_reverse(int, int) override;
|
||||
double compute_scalar() override;
|
||||
double compute_vector(int) override;
|
||||
double compute_array(int, int) override;
|
||||
int modify_param(int, char **) override;
|
||||
int modify_param(const std::string &);
|
||||
void init() override;
|
||||
@ -104,8 +104,6 @@ class FixElectrodeConp : public Fix {
|
||||
void read_from_file(std::string input_file, double **, const std::string &);
|
||||
void compute_sd_vectors();
|
||||
void compute_sd_vectors_ffield();
|
||||
std::vector<int> setvars_types, setvars_groups, setvars_vars;
|
||||
void update_setvars(int);
|
||||
int groupnum_from_name(char *);
|
||||
double evscale;
|
||||
class Pair *pair;
|
||||
|
||||
Reference in New Issue
Block a user