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Merge branch 'develop' into plumed-plugin

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This commit is contained in:
Axel Kohlmeyer
2024-07-30 20:30:21 -04:00
parent 185141bd7d a54e67bf1c
commit cb00839357
487 changed files with 26476 additions and 6758 deletions
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4
examples/PACKAGES/cgspica/sds-monolayer/in.sds-regular
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@ -5,9 +5,9 @@ dimension 3
atom_style full
processors * * 1
pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long"
pair_style lj/spica/coul/long 15.0
bond_style harmonic
angle_style sdk # compatible with "spica"
angle_style spica
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz

1
examples/PACKAGES/electrode/madelung/.gitignore vendored
View File

@ -1,2 +1,3 @@
*.csv
*.txt
*.lammpstrj

18
examples/PACKAGES/electrode/madelung/eval.py
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@ -17,14 +17,22 @@ q_ref = float(ref_line[3])
inv11_ref = float(ref_line[4])
inv12_ref = float(ref_line[5])
b1_ref = float(ref_line[6])
felec1_ref = float(ref_line[8])
felyt1_ref = float(ref_line[10])
press_ref = float(ref_line[12])
# out.csv
with open(sys.argv[2]) as f:
out_line = f.readlines()[-1].split(", ")
e_out = float(out_line[0])
q_out = float(out_line[1])
press_out = float(out_line[2])
out_lines = [("energy", e_ref, e_out), ("charge", q_ref, q_out)]
out_lines = [
("energy", e_ref, e_out),
("charge", q_ref, q_out),
("pressure", press_ref, press_out),
]
# vec.csv
vec_file = "vec.csv"
@ -44,6 +52,14 @@ if op.isfile(inv_file):
inv12_out = float(inv_line[1])
out_lines.append(("inv11", inv11_ref, inv11_out))
# forces.lammpstrj
force_file = "forces.lammpstrj"
with open(force_file) as f:
lines = f.readlines()[9:]
for name, i, f_ref in [("felec1", "1", felec1_ref), ("felyt1", "3", felyt1_ref)]:
f_out = next(float(y[3]) for x in lines if (y := x.split()) and y[0] == i)
out_lines.append((name, f_ref, f_out))
lines = []
for label, ref, out in out_lines:
error = rel_error(out, ref)

2
examples/PACKAGES/electrode/madelung/in.eta_cg
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@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
fix feta all property/atom d_eta ghost on
set group bot d_eta 0.5
set group top d_eta 3.0
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta algo cg 1e-6
fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta algo cg 1e-6
run 0

2
examples/PACKAGES/electrode/madelung/in.eta_mix
View File

@ -8,7 +8,7 @@ thermo_style custom step pe c_qbot c_qtop
fix feta all property/atom d_eta ghost on
set group bot d_eta 0.5
set group top d_eta 3.0
fix conp bot electrode/conp 0 2 couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
fix conp bot electrode/conp 0 NULL couple top 1 symm on eta d_eta write_inv inv.csv write_vec vec.csv
run 0

98
examples/PACKAGES/electrode/madelung/plate_cap.py
View File

@ -1,12 +1,17 @@
#!/usr/bin/env python3
import time
import numpy as np
from scipy.special import erf
SQRT2 = np.sqrt(2)
SQRTPI_INV = 1 / np.sqrt(np.pi)
COULOMB = 332.06371 # Coulomb constant in Lammps 'real' units
QE2F = 23.060549
NKTV2P = 68568.415 # pressure in 'real' units
LENGTH = 10000 # convergence parameter
LZ = 20
def lattice(length):
@ -26,6 +31,25 @@ def b_element(r, q, eta):
return q * erf(eta * r) / r
def force_gauss(r, qq, eta):
etar = eta * r
return (qq / np.square(r)) * (
erf(etar) - 2 * etar * SQRTPI_INV * np.exp(-np.square(etar))
)
def force_point(r, qq):
return qq / np.square(r)
def force_component(dx, d, qq, eta=None):
if eta:
return np.sum(dx / d * force_gauss(d, qq, eta))
else:
return np.sum(dx / d * force_point(d, qq))
time_start = time.perf_counter()
a = 1 # nearest neighbor distance i.e. lattice constant / sqrt(2)
x_elec = [-2, 2]
x_elyt = [-1, 1]
@ -36,8 +60,20 @@ 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)
image_distances = []
for x in x_elec:
image_distances.append([])
for y in x_elyt:
image_distances[-1].append(np.sqrt(np.square(distances) + np.abs(y - x) ** 2))
image_elyt_distances = [[None for _ in range(len(x_elyt))] for _ in range(len(x_elyt))]
for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
image_elyt_distances[i][j] = np.sqrt(
np.square(distances) + np.abs(xj - xi) ** 2
)
for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
# for name, eta_elec in [("", [2.0, 2.0])]:
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]
@ -55,22 +91,18 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
# electrode-electrolyte interaction
b = []
for x, eta in zip(x_elec, eta_elec):
for i, (x, eta) in enumerate(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))
for j, (y, q) in enumerate(zip(x_elyt, q_elyt)):
bi += b_element(np.abs(y - x), q, eta)
bi += 4 * np.sum(b_element(image_distances[i][j], 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_12 = 1 / distance_elyt + 4 * np.sum(1 / image_elyt_distances[0][1])
elyt = np.array([[elyt_11, elyt_12], [elyt_12, elyt_11]])
energy_elyt = 0.5 * np.dot(q_elyt, np.dot(elyt, q_elyt))
@ -78,9 +110,48 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
q = np.dot(inv, v - b)
energy = COULOMB * (0.5 * np.dot(q, np.dot(A, q)) + np.dot(b, q) + energy_elyt)
# forces in out-of-plane direction
f_elec = np.zeros(len(x_elec))
f_elyt = np.zeros(len(x_elyt))
# electrode-electrode
dx = x_elec[1] - x_elec[0]
fij_box = force_component(dx, np.abs(dx), q[0] * q[1], eta_mix)
fij_img = 4 * force_component(dx, opposite_distances, q[0] * q[1], eta_mix)
f_elec[0] -= fij_box + fij_img
f_elec[1] += fij_box + fij_img
# electrode-electrolyte
for i, (xi, qi, etai) in enumerate(zip(x_elec, q, eta_elec)):
for j, (xj, qj) in enumerate(zip(x_elyt, q_elyt)):
dx = xj - xi
fij_box = force_component(dx, np.abs(dx), qi * qj, etai)
fij_img = 4 * force_component(dx, image_distances[i][j], qi * qj, etai)
f_elec[i] -= fij_box + fij_img
f_elyt[j] += fij_box + fij_img
# electrolyte-electrolyte
for i, (xi, qi) in enumerate(zip(x_elyt, q_elyt)):
for j, (xj, qj) in list(enumerate(zip(x_elyt, q_elyt)))[i + 1 :]:
dx = xj - xi
fij_box = force_component(dx, np.abs(dx), qi * qj)
fij_img = 4 * force_component(dx, image_elyt_distances[i][j], qi * qj)
f_elyt[i] -= fij_img + fij_box
f_elyt[j] += fij_img + fij_box
# force units
assert np.abs(np.sum(f_elec) + np.sum(f_elyt)) < 1e-8
f_elec *= COULOMB
f_elyt *= COULOMB
# Virial
volume = a**2 * LZ
virial = 0.0
for x, f in [(x_elec, f_elec), (x_elyt, f_elyt)]:
virial += np.dot(x, f)
pressure = NKTV2P * virial / volume
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"
"length, energy / kcal/mol, q1 / e, q2 / e, inv11 / A, inv12 / A"
+ ", b1 / e/A, b2 / e/A, felec1 / kcal/mol/A, felec2 / kcal/mol/A"
+ ", felyt1 / kcal/mol/A, felyt2 / kcal/mol/A, press\n"
)
f.write(
", ".join(
@ -93,7 +164,14 @@ for name, eta_elec in [("", [2.0, 2.0]), ("_eta_mix", [0.5, 3.0])]:
f"{inv[0, 1]:.10f}",
f"{b[0]:.8f}",
f"{b[1]:.8f}",
f"{f_elec[0]:.5f}",
f"{f_elec[1]:.5f}",
f"{f_elyt[0]:.5f}",
f"{f_elyt[1]:.5f}",
f"{pressure:.2f}",
]
)
+ "\n"
)
time_end = time.perf_counter()
print(f"{time_end - time_start:0.4f} seconds")

6
examples/PACKAGES/electrode/madelung/settings.mod
View File

@ -19,4 +19,8 @@ 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}, ${charge}" file "out.csv"
compute press all pressure NULL virial
variable p3 equal c_press[3]
fix fxprint all print 1 "${vpe}, ${charge}, ${p3}" file "out.csv"
dump dump_forces all custom 1 forces.lammpstrj id fx fy fz

4064
examples/PACKAGES/electrode/piston/data.piston.final
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File diff suppressed because it is too large Load Diff

6
examples/PACKAGES/electrode/piston/in.piston
View File

@ -42,7 +42,11 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxdrag wall viscous 100
fix fxrigid wall rigid/nve single

97
examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.1 → examples/PACKAGES/electrode/piston/log.22May2024.piston.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (3 Nov 2022)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
using 1 OpenMP thread(s) per MPI task
# The intention is to find the average position of one wall at atmospheric
# pressure. The output is the wall position over time which can be used to
# find the average position for a run with fixed wall position.
@ -40,8 +41,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.011 seconds
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
# ----------------- Settings Section -----------------
@ -77,7 +78,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
Wall force per atom: -0.000109285996244287
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxpressure wall aveforce 0 0 -0.000109285996244287
fix fxdrag wall viscous 100
fix fxrigid wall rigid/nve single
1 rigid bodies with 48 atoms
@ -134,7 +141,7 @@ PPPM/electrode initialization ...
stencil order = 5
estimated absolute RMS force accuracy = 0.02930901
estimated relative force accuracy = 8.8263214e-05
using double precision MKL FFT
using double precision FFTW3
3d grid and FFT values/proc = 15884 6480
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
@ -157,54 +164,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes
Step c_temp_mobile c_qwa c_qau v_top_wall
0 303.38967 -0.042963484 0.042963484 21.4018
5000 285.08828 -0.26105255 0.26105255 25.155629
10000 323.19176 -0.26264003 0.26264003 24.541676
15000 310.479 -0.27318148 0.27318148 23.141522
20000 295.18544 -0.11313444 0.11313444 23.828735
25000 295.38607 -0.25433086 0.25433086 23.673314
30000 288.0613 -0.30099901 0.30099901 23.438086
35000 278.5591 -0.15823576 0.15823576 24.311915
40000 303.95751 -0.19941381 0.19941381 23.69594
45000 279.026 -0.1659962 0.1659962 23.588604
50000 298.79278 -0.28866703 0.28866703 23.372508
55000 301.03353 -0.078370381 0.078370381 23.192985
60000 306.77965 -0.12807205 0.12807205 23.968574
65000 309.86008 -0.27162663 0.27162663 23.616704
70000 287.31116 -0.029751882 0.029751882 23.667495
75000 312.48654 -0.10759866 0.10759866 23.504105
80000 309.94267 -0.2558548 0.2558548 23.810576
85000 328.04389 -0.1575471 0.1575471 24.013437
90000 302.9806 -0.032002164 0.032002164 24.264432
95000 294.20804 -0.27797238 0.27797238 23.291758
100000 307.63019 -0.19047448 0.19047448 23.632147
Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms
5000 311.85363 0.03543775 -0.03543775 24.79665
10000 285.91321 -0.16873703 0.16873703 23.103088
15000 295.39476 -0.44424612 0.44424612 23.767107
20000 296.12969 -0.14120993 0.14120993 23.96361
25000 306.59629 -0.29333182 0.29333182 23.884488
30000 297.98559 -0.10749684 0.10749684 23.73316
35000 297.98503 -0.11809975 0.11809975 23.984669
40000 300.26292 -0.32784184 0.32784184 23.462748
45000 295.68441 -0.25940165 0.25940165 23.516403
50000 315.12883 -0.36037614 0.36037614 23.627879
55000 290.55151 -0.0032838106 0.0032838106 23.684931
60000 316.4625 -0.17245368 0.17245368 24.126883
65000 296.79343 -0.054061851 0.054061851 23.695094
70000 305.99923 -0.11363801 0.11363801 23.55476
75000 297.40131 -0.27054153 0.27054153 23.928994
80000 306.54811 -0.25409719 0.25409719 23.869448
85000 303.95231 -0.17895561 0.17895561 23.658833
90000 313.43739 -0.059036514 0.059036514 23.36056
95000 290.3077 -0.31394478 0.31394478 23.885538
100000 297.5156 -0.30730083 0.30730083 23.511674
Loop time of 1586.06 on 1 procs for 100000 steps with 726 atoms
Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 10.895 ns/day, 2.203 hours/ns, 63.049 timesteps/s, 45.774 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 190.47 | 190.47 | 190.47 | 0.0 | 35.88
Bond | 0.10754 | 0.10754 | 0.10754 | 0.0 | 0.02
Kspace | 73.179 | 73.179 | 73.179 | 0.0 | 13.79
Neigh | 24.209 | 24.209 | 24.209 | 0.0 | 4.56
Comm | 1.6857 | 1.6857 | 1.6857 | 0.0 | 0.32
Output | 0.0016861 | 0.0016861 | 0.0016861 | 0.0 | 0.00
Modify | 240.23 | 240.23 | 240.23 | 0.0 | 45.26
Other | | 0.9595 | | | 0.18
Pair | 460.91 | 460.91 | 460.91 | 0.0 | 29.06
Bond | 0.047873 | 0.047873 | 0.047873 | 0.0 | 0.00
Kspace | 341.4 | 341.4 | 341.4 | 0.0 | 21.53
Neigh | 52.868 | 52.868 | 52.868 | 0.0 | 3.33
Comm | 5.2321 | 5.2321 | 5.2321 | 0.0 | 0.33
Output | 0.00099102 | 0.00099102 | 0.00099102 | 0.0 | 0.00
Modify | 724.63 | 724.63 | 724.63 | 0.0 | 45.69
Other | | 0.9741 | | | 0.06
Nlocal: 726 ave 726 max 726 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2335 ave 2335 max 2335 min
Nghost: 2336 ave 2336 max 2336 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 120271 ave 120271 max 120271 min
Neighs: 120321 ave 120321 max 120321 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 120271
Ave neighs/atom = 165.66253
Total # of neighbors = 120321
Ave neighs/atom = 165.7314
Ave special neighs/atom = 1.7355372
Neighbor list builds = 7722
Neighbor list builds = 7670
Dangerous builds = 0
write_data "data.piston.final"
System init for write_data ...
@ -213,11 +220,11 @@ PPPM/electrode initialization ...
G vector (1/distance) = 0.32814871
grid = 12 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.029311365
estimated relative force accuracy = 8.8270304e-05
using double precision MKL FFT
estimated absolute RMS force accuracy = 0.029311329
estimated relative force accuracy = 8.8270197e-05
using double precision FFTW3
3d grid and FFT values/proc = 15884 6480
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Average conjugate gradient steps: 1.981
Total wall time: 0:08:50
Total wall time: 0:26:26

109
examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.4 → examples/PACKAGES/electrode/piston/log.22May2024.piston.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (3 Nov 2022)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
using 1 OpenMP thread(s) per MPI task
# The intention is to find the average position of one wall at atmospheric
# pressure. The output is the wall position over time which can be used to
# find the average position for a run with fixed wall position.
@ -41,8 +42,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.017 seconds
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
# ----------------- Settings Section -----------------
@ -66,7 +67,7 @@ Finding SHAKE clusters ...
0 = # of size 3 clusters
0 = # of size 4 clusters
210 = # of frozen angles
find clusters CPU = 0.002 seconds
find clusters CPU = 0.000 seconds
pair_modify mix arithmetic
# ----------------- Run Section -----------------
@ -78,7 +79,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
Wall force per atom: -0.000109285996244287
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxpressure wall aveforce 0 0 -0.000109285996244287
fix fxdrag wall viscous 100
fix fxrigid wall rigid/nve single
1 rigid bodies with 48 atoms
@ -135,7 +142,7 @@ PPPM/electrode initialization ...
stencil order = 5
estimated absolute RMS force accuracy = 0.02930901
estimated relative force accuracy = 8.8263214e-05
using double precision MKL FFT
using double precision FFTW3
3d grid and FFT values/proc = 8512 2880
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
@ -158,54 +165,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.22 | 10.41 Mbytes
Step c_temp_mobile c_qwa c_qau v_top_wall
0 303.38967 -0.042963484 0.042963484 21.4018
5000 292.03027 -0.19040435 0.19040435 24.581338
10000 309.52764 -0.48308301 0.48308301 23.776985
15000 295.00243 -0.16591109 0.16591109 23.672038
20000 293.5536 -0.086669084 0.086669084 23.426455
25000 303.0079 -0.16488112 0.16488112 23.862966
30000 306.31463 -0.23192653 0.23192653 23.819882
35000 303.66268 -0.2317907 0.2317907 23.495344
40000 301.39435 -0.34661329 0.34661329 23.657835
45000 291.61205 -0.30539427 0.30539427 23.437303
50000 298.65319 -0.096107034 0.096107034 23.57809
55000 282.65069 -0.14943539 0.14943539 23.823728
60000 310.64182 -0.17418813 0.17418813 23.286959
65000 308.47141 -0.02075662 0.02075662 23.91313
70000 292.5186 -0.080163162 0.080163162 23.96283
75000 270.13928 -0.029528648 0.029528648 23.488972
80000 322.10914 0.030761045 -0.030761045 23.47592
85000 310.60347 -0.24069996 0.24069996 23.987091
90000 294.35695 -0.070458235 0.070458235 23.397929
95000 308.69043 -0.2652581 0.2652581 23.473813
100000 318.71883 0.024035956 -0.024035956 23.449863
Loop time of 590.232 on 4 procs for 100000 steps with 726 atoms
5000 291.6303 -0.1820085 0.1820085 24.641399
10000 299.42886 -0.19823095 0.19823095 23.820522
15000 288.23071 -0.065261869 0.065261869 23.360845
20000 299.4644 -0.042993777 0.042993777 23.987554
25000 304.26497 -0.15665293 0.15665293 23.729006
30000 292.29674 -0.25142779 0.25142779 23.960725
35000 295.57492 -0.01269228 0.01269228 23.445383
40000 303.38438 -0.13941727 0.13941727 23.517483
45000 302.211 -0.19589892 0.19589892 23.704043
50000 281.64939 -0.18057298 0.18057298 23.542137
55000 274.90565 -0.15453379 0.15453379 23.734347
60000 290.70459 -0.27977436 0.27977436 23.835365
65000 293.42241 -0.2454241 0.2454241 23.59269
70000 295.20229 -0.041314995 0.041314995 23.73856
75000 297.79519 -0.11231755 0.11231755 23.57262
80000 285.17858 -0.070796508 0.070796508 23.817135
85000 311.71609 -0.068920177 0.068920177 23.861127
90000 287.80446 -0.19183387 0.19183387 23.369393
95000 309.43345 -0.15238671 0.15238671 23.597792
100000 294.12422 -0.14284353 0.14284353 23.526286
Loop time of 876.546 on 4 procs for 100000 steps with 726 atoms
Performance: 29.277 ns/day, 0.820 hours/ns, 169.425 timesteps/s, 123.003 katom-step/s
72.5% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 19.714 ns/day, 1.217 hours/ns, 114.084 timesteps/s, 82.825 katom-step/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 57.391 | 75.867 | 96.292 | 212.1 | 12.85
Bond | 0.10177 | 0.11042 | 0.12415 | 2.7 | 0.02
Kspace | 102.79 | 123.16 | 141.5 | 165.7 | 20.87
Neigh | 12.808 | 12.895 | 12.982 | 2.3 | 2.18
Comm | 18.885 | 19.973 | 21.064 | 24.0 | 3.38
Output | 0.0022573 | 0.0022749 | 0.0023225 | 0.1 | 0.00
Modify | 355.89 | 356.74 | 357.61 | 4.2 | 60.44
Other | | 1.478 | | | 0.25
Pair | 123.63 | 171.23 | 215.73 | 336.6 | 19.53
Bond | 0.068261 | 0.075883 | 0.081822 | 1.9 | 0.01
Kspace | 187.59 | 231.71 | 279.01 | 287.1 | 26.43
Neigh | 29.28 | 29.462 | 29.637 | 2.5 | 3.36
Comm | 12.544 | 13.731 | 14.929 | 29.1 | 1.57
Output | 0.0010182 | 0.0014585 | 0.0016071 | 0.7 | 0.00
Modify | 428.74 | 429.25 | 429.74 | 2.3 | 48.97
Other | | 1.092 | | | 0.12
Nlocal: 181.5 ave 207 max 169 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 1961.5 ave 1984 max 1926 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 30051 ave 41646 max 20775 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nlocal: 181.5 ave 195 max 166 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 1955.5 ave 1978 max 1931 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 30343 ave 39847 max 20428 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 120204
Ave neighs/atom = 165.57025
Total # of neighbors = 121372
Ave neighs/atom = 167.17906
Ave special neighs/atom = 1.7355372
Neighbor list builds = 7663
Neighbor list builds = 7698
Dangerous builds = 0
write_data "data.piston.final"
System init for write_data ...
@ -214,11 +221,11 @@ PPPM/electrode initialization ...
G vector (1/distance) = 0.32814871
grid = 12 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.029311028
estimated relative force accuracy = 8.8269289e-05
using double precision MKL FFT
estimated absolute RMS force accuracy = 0.029310954
estimated relative force accuracy = 8.8269069e-05
using double precision FFTW3
3d grid and FFT values/proc = 8512 2880
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Average conjugate gradient steps: 1.982
Total wall time: 0:09:50
Average conjugate gradient steps: 1.981
Total wall time: 0:14:36