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updated doc pages and code

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This commit is contained in:
Steve Plimpton
2025-05-19 14:34:22 -06:00
parent ebfb94a717
commit c3b25c8c27
12 changed files with 512 additions and 338 deletions
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4
examples/python/in.python.wrap
View File

@ -25,11 +25,10 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve
variable foo python truncate
python truncate return v_foo input 1 v_pyarg1 format fi here """
python truncate return v_foo input 1 iv_arg format fi here """
def truncate(x):
return int(x)
"""
variable pyarg1 internal 0.0
variable scalar equal py_foo(4.5)
print "TRUNCATE ${scalar}"
@ -40,7 +39,6 @@ variable ztrunc atom py_foo(z)
# examine dump file to see truncated xyz coords of each atom
#dump 1 all custom 100 tmp.dump id x y z
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
run 100

24
examples/python/log.1May25.python.wrap.g++.1
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@ -1,4 +1,4 @@
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-125-g7ca493917a-modified)
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified)
# 3d Lennard-Jones melt with equal- and atom-style variables which
# use a Python function wrapper in their formulas
@ -35,11 +35,10 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve
variable foo python truncate
python truncate return v_foo input 1 v_pyarg1 format fi here """
python truncate return v_foo input 1 iv_arg format fi here """
def truncate(x):
return int(x)
"""
variable pyarg1 internal 0.0
variable scalar equal py_foo(4.5)
print "TRUNCATE ${scalar}"
@ -49,7 +48,8 @@ variable xtrunc atom py_foo(x)
variable ytrunc atom py_foo(y)
variable ztrunc atom py_foo(z)
#dump 1 all custom 100 tmp.dump id x y z
# examine dump file to see truncated xyz coords of each atom
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
run 100
@ -70,20 +70,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
100 0.75627408 -5.7580082 0 -4.6258659 0.21870071
Loop time of 0.0160255 on 1 procs for 100 steps with 500 atoms
Loop time of 0.014627 on 1 procs for 100 steps with 500 atoms
Performance: 2695709.610 tau/day, 6240.069 timesteps/s, 3.120 Matom-step/s
Performance: 2953445.899 tau/day, 6836.680 timesteps/s, 3.418 Matom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.011326 | 0.011326 | 0.011326 | 0.0 | 70.67
Neigh | 0.002924 | 0.002924 | 0.002924 | 0.0 | 18.25
Comm | 0.00046255 | 0.00046255 | 0.00046255 | 0.0 | 2.89
Output | 0.0010398 | 0.0010398 | 0.0010398 | 0.0 | 6.49
Modify | 0.00020589 | 0.00020589 | 0.00020589 | 0.0 | 1.28
Other | | 6.725e-05 | | | 0.42
Pair | 0.010546 | 0.010546 | 0.010546 | 0.0 | 72.10
Neigh | 0.0027775 | 0.0027775 | 0.0027775 | 0.0 | 18.99
Comm | 0.00044818 | 0.00044818 | 0.00044818 | 0.0 | 3.06
Output | 0.00060601 | 0.00060601 | 0.00060601 | 0.0 | 4.14
Modify | 0.00018516 | 0.00018516 | 0.00018516 | 0.0 | 1.27
Other | | 6.39e-05 | | | 0.44
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0

26
examples/python/log.1May25.python.wrap.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-125-g7ca493917a-modified)
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified)
# 3d Lennard-Jones melt with equal- and atom-style variables which
# use a Python function wrapper in their formulas
@ -35,11 +35,10 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve
variable foo python truncate
python truncate return v_foo input 1 v_pyarg1 format fi here """
python truncate return v_foo input 1 iv_arg format fi here """
def truncate(x):
return int(x)
"""
variable pyarg1 internal 0.0
variable scalar equal py_foo(4.5)
print "TRUNCATE ${scalar}"
@ -49,7 +48,8 @@ variable xtrunc atom py_foo(x)
variable ytrunc atom py_foo(y)
variable ztrunc atom py_foo(z)
#dump 1 all custom 100 tmp.dump id x y z
# examine dump file to see truncated xyz coords of each atom
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
run 100
@ -70,20 +70,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
100 0.75627408 -5.7580082 0 -4.6258659 0.21870071
Loop time of 0.00641075 on 4 procs for 100 steps with 500 atoms
Loop time of 0.0062374 on 4 procs for 100 steps with 500 atoms
Performance: 6738684.275 tau/day, 15598.806 timesteps/s, 7.799 Matom-step/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 6925957.189 tau/day, 16032.308 timesteps/s, 8.016 Matom-step/s
74.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0028061 | 0.0028831 | 0.0029657 | 0.1 | 44.97
Neigh | 0.00086635 | 0.00088279 | 0.00089739 | 0.0 | 13.77
Comm | 0.0020095 | 0.0020768 | 0.0021521 | 0.1 | 32.40
Output | 0.00041634 | 0.00042457 | 0.00043221 | 0.0 | 6.62
Modify | 6.2967e-05 | 6.4188e-05 | 6.5205e-05 | 0.0 | 1.00
Other | | 7.934e-05 | | | 1.24
Pair | 0.0027648 | 0.0028431 | 0.0029465 | 0.1 | 45.58
Neigh | 0.00084567 | 0.00086563 | 0.00088168 | 0.0 | 13.88
Comm | 0.0020822 | 0.0021609 | 0.0022418 | 0.1 | 34.64
Output | 0.00021567 | 0.00022125 | 0.00022624 | 0.0 | 3.55
Modify | 6.2567e-05 | 6.4105e-05 | 6.63e-05 | 0.0 | 1.03
Other | | 8.241e-05 | | | 1.32
Nlocal: 125 ave 126 max 123 min
Histogram: 1 0 0 0 0 0 1 0 0 2