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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14683 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2016-02-26 15:49:30 +00:00
parent 4351bad69f
commit 2a157729a3
10 changed files with 2 additions and 820 deletions
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2
doc/Section_packages.html
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@ -507,7 +507,7 @@ name links to a sub-section below with more details.</p>
<td>python</td>
<td>lib/python</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="Section_tools.html#reax"><span>REAX</span></a></td>
<td>ReaxFF potential</td>
<td>Aidan Thompson (Sandia)</td>
<td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>

2
doc/_sources/Manual.txt
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@ -5,7 +5,7 @@
LAMMPS Documentation
====================
22 Feb 2016 version
25 Feb 2016 version
-------------------
Version info:

235
regress/benchmark.py
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@ -1,235 +0,0 @@
#!/usr/bin/env python
"""
function: numerical comparisions of logs and corresponding benchmarks
usage: benchmark.py <nprocs> <njobs> <dirs>
"""
import sys
import os
import math
import re
from operator import itemgetter
from glob import glob
import time
import multiprocessing as mp
try:
import Queue as queue # 2.6
except ImportError:
import queue # 3.0
#====================================================
### constants
#====================================================
thermo_pattern = re.compile("^Step "); # fragile
data_pattern = re.compile("\s*\d"); # fragile
fail_pattern = re.compile("FAIL");
tol = 1.e-6 # 1.e-10
arch = "openmpi"
src_path = "../src/" #relative to home
exe_path = "../"+src_path
#====================================================
### date
#====================================================
def date():
return time.asctime()
#====================================================
### timer
#====================================================
## NOTE these don't seem to work how I expect them to
def start():
global dt
dt = -(time.clock())
def stop():
global dt
dt += (time.clock())
return dt
#====================================================
### run a benchmark
#====================================================
def run_test(test):
input = "in."+test;
log = "log."+test
stdout = "stdout."+test
ref = (glob(log+"*."+str(np)))[0];
msg = "==== comparing "+log+" with "+ref+" ====\n"
if (os.path.isfile(log)): os.remove(log)
if (os.path.isfile(stdout)): os.remove(stdout)
os.system(lmps+input+" >& "+stdout);
if (not os.path.isfile(log)) :
msg += "!!! no "+log+"\n";
msg += "!!! test "+test+" FAILED\n"
return msg
[cdict,cdata] = extract_data(log);
[bdict,bdata] = extract_data(ref);
cols = range(len(bdict))
if (len(cdata) != len(bdata)):
msg += "!!! data size "+str(len(cdata))+" does not match data "+str(len(bdata))+" in "+ref+"\n";
msg += "!!! test "+test+" FAILED\n"
return msg
fail = False
i = 0
for name in bdict:
[passing,cmsg] = compare(name,cdata[cols[i]],bdata[cols[i]]);
i += 1
msg += cmsg
if (not passing) : fail = True
if (fail) :
msg += "!!! test "+test+" FAILED\n"
else :
msg += "*** test "+test+" passed\n"
return msg
#====================================================
### extract data from log file
#====================================================
def extract_data(file):
dictionary = [];
data = []
read = False
for line in open(file):
if (read and data_pattern.match(line)) :
cols = line.split();
data.append(cols)
else :
read = False
if (thermo_pattern.match(line)):
dictionary = line.split();
read = True
return [dictionary,data]
#====================================================
### compare columns of current and benchmark
#====================================================
def compare(name,col1,col2):
err = 0.
norm1 = 0.
norm2 = 0.
n = len(col2)
for i in range(n):
v1 = float(col1[i])
v2 = float(col2[i])
norm1 += v1*v1
norm2 += v2*v2
dv = v1-v2
err += dv*dv
norm1 /= n
norm2 /= n
err /= n
if (norm2 > tol) :
msg = "{0:7s} relative error {1:4} wrt norm {2:7}\n".format(name,err,norm2)
else :
msg = "{0:7s} error {1:4}\n" .format(name,err)
return [(err < tol),msg];
#################################################################
class Worker(mp.Process):
def __init__(self, work_queue, result_queue):
mp.Process.__init__(self)
self.work_queue = work_queue
self.result_queue = result_queue
def run(self):
while True:
try:
job = self.work_queue.get_nowait()
except queue.Empty:
break
#print(">>> starting " + str(job[1]) + " ...")
os.chdir(job[0])
start()
msg = run_test(job[1])
elapsed_time = stop()
msg += "elapsed time "+str(elapsed_time)+"\n"
os.chdir(home)
self.result_queue.put([job[1],msg])
#====================================================
### parse
#====================================================
def init() :
global np, njobs, ntests, lmps, arch, home
home = os.getcwd()
if (len(sys.argv) < 4) :
print "usage: benchmark.py <nprocs> <njobs> <test_dirs>"
sys.exit(1)
np = int(sys.argv[1])
njobs = int(sys.argv[2])
lmps = "../"+src_path+"lmp_"+arch+" -in "
if (np > 1):
lmps = "mpirun -np "+str(np)+" "+lmps
else:
arch = "serial"
lmps = exe_path+"lmp_"+arch+" -in "
pool = mp.Pool(njobs)
dirs = sys.argv[3:]
tests = []
for dir in dirs:
os.chdir(dir);
for path in glob("./in.*"):
test = path[5:];
tests.append([dir,test])
os.chdir(home)
ntests = len(tests)
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
print "start: ",date()
print "arch:",arch,
print "nprocs:",np
print "ntests:",ntests,
print "njobs:",njobs
print "relative tolerance:",tol
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
print
return tests
#====================================================
### build executable
#====================================================
def build(arch):
os.system("cd ..; svn update >& svn_update.log")
os.system("cd ../src; make no-atc >& /dev/null")
os.system("cd ../src; make clean-all >& /dev/null")
#os.system("cd ../src; make yes-all >& /dev/null")
os.system("cd ../src; make yes-dipole >& /dev/null")
sys.stdout.flush()
print "** building ",arch,"...",
os.system("cd "+src_path+"; make -j "+str(np)+" "+arch+" >& build_"+arch+".log")
if (not os.path.isfile(src_path+"lmp_"+arch)) :
print "!!! build ",arch," FAILED"
sys.exit()
else:
print "done"
print
#====================================================
### main
#====================================================
if __name__ == '__main__':
tests = init()
build(arch)
work_queue = mp.Queue()
for test in tests:
work_queue.put(test)
result_queue = mp.Queue()
nfails = 0
fail_list = []
for i in range(njobs):
w = Worker(work_queue, result_queue)
w.start()
for i in range(ntests):
[test,msg] = result_queue.get()
if (fail_pattern.search(msg)) :
nfails += 1
fail_list.append(test)
#print msg # can print only if failed
print msg # can print only if failed
#print test, " passed"
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
print "end:",date()
if (nfails == 0):
print "*** no failures ***"
else :
print "!!!",nfails,"of",ntests,"tests failed"
for test in fail_list:
print test
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"

20
regress/melt/in.melt
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@ -1,20 +0,0 @@
# author: sjplimp@sandia.gov
# packaged:
# 3d Lennard-Jones melt
log log.melt
thermo_modify format float %22.16g
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
thermo 50
run 250

60
regress/melt/log.melt.linux.4
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@ -1,60 +0,0 @@
LAMMPS (18 Feb 2013)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 1 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
thermo 50
run 250
Memory usage per processor = 1.89067 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.214934 on 4 procs for 250 steps with 4000 atoms
Pair time (%) = 0.159902 (74.3957)
Neigh time (%) = 0.021036 (9.78721)
Comm time (%) = 0.0281214 (13.0837)
Outpt time (%) = 0.000122249 (0.0568775)
Other time (%) = 0.00575262 (2.67646)
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds = 0

26
regress/min/in.min
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@ -1,26 +0,0 @@
# author: sjplimp@sandia.gov
# packages:
# 2d Lennard-Jones melt and subsequent energy minimization
log log.min
thermo_modify format float %22.16g
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
thermo 100
run 1000
neigh_modify delay 0 every 1 check yes
thermo 50
minimize 1.0e-6 0.001 1000 10000

31
regress/min/in.min.box
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@ -1,31 +0,0 @@
# author: sjplimp@sandia.gov
# packages:
# 2d Lennard-Jones melt and subsequent energy minimization
log log.min.box
thermo_modify format float %22.16g
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
thermo_style custom step temp pe pxx pyy pxy
create_atoms 1 box
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
thermo 100
run 1000
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
thermo 50
minimize 1.0e-6 0.001 1000 10000
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000

335
regress/min/log.min.box.linux.4
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@ -1,335 +0,0 @@
thermo_modify format float %22.16g
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
thermo_style custom step temp pe pxx pyy pxy
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:664)
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
thermo 100
run 1000
Memory usage per processor = 2.06131 Mbytes
Step Temp PotEng Pxx Pyy Pxy
0 5 -2.461717 4.8446721 5.1934297 -0.021185605
100 3.2788864 -0.74311698 15.13728 16.688385 -0.13039086
200 3.3041082 -0.77000277 15.112653 16.092652 -0.15719124
300 3.3840228 -0.84859211 15.866192 14.510214 0.43596695
400 3.3916063 -0.85694601 15.440117 15.327588 -0.40886736
500 3.3136052 -0.77935264 15.526339 16.140252 0.14800908
600 3.3888915 -0.85213742 15.009217 15.3163 0.2544259
700 3.2123632 -0.67641807 16.052563 16.56862 -0.40174504
800 3.3016497 -0.76571656 15.797225 15.48117 -0.066795543
900 3.4621454 -0.9260857 14.547941 14.997988 0.52470514
1000 3.2803075 -0.74465936 16.254614 15.41658 -0.58853939
Loop time of 0.150018 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.0741317 (49.4152)
Neigh time (%) = 0.0260313 (17.3521)
Comm time (%) = 0.0371104 (24.7373)
Outpt time (%) = 0.000306547 (0.20434)
Other time (%) = 0.0124381 (8.29105)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 170.25 ave 176 max 167 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 1936.75 ave 1963 max 1896 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.75261 Mbytes
Step Temp PotEng Pxx Pyy Pxy
1000 0 -0.74465936 13.356463 12.783183 -0.38683262
1050 0 -2.8198371 -1.1342845 -1.0864736 0.038082467
1100 0 -2.8554989 -1.0568419 -1.1603959 0.013709853
1150 0 -2.8646695 -1.0162886 -1.1061819 0.021389354
1200 0 -2.8688213 -1.0541419 -1.0929891 0.0028248833
1250 0 -2.8764988 -1.0459176 -1.0959241 0.049805
1300 0 -2.8776606 -1.0530918 -1.1141788 0.05731449
1350 0 -2.8789379 -1.0481324 -1.1404108 0.035720707
1365 0 -2.879076 -1.0493949 -1.1436932 0.037565201
Loop time of 0.23541 on 4 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.744659361981 -2.87907436106 -2.8790759758
Force two-norm initial, final = 2006.88 0.477401
Force max component initial, final = 395.193 0.0879763
Final line search alpha, max atom move = 0.00334856 0.000294593
Iterations, force evaluations = 365 1437
Pair time (%) = 0.15347 (65.1926)
Neigh time (%) = 0.00975943 (4.14572)
Comm time (%) = 0.0477005 (20.2627)
Outpt time (%) = 0.000189364 (0.0804402)
Other time (%) = 0.0242908 (10.3185)
Nlocal: 200 ave 204 max 194 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 171.75 ave 173 max 170 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1762.75 ave 1797 max 1711 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 7051
Ave neighs/atom = 8.81375
Neighbor list builds = 78
Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
Memory usage per processor = 2.75261 Mbytes
Step Temp PotEng Pxx Pyy Pxy
1365 0 -2.879076 -1.0493949 -1.1436932 0.037565201
1400 0 -2.8859021 -0.86433583 -0.91383427 0.038857701
1450 0 -2.8929425 -0.58254768 -0.55566103 0.040538566
1500 0 -2.8966088 -0.28118754 -0.15988163 0.042020855
1550 0 -2.8967125 0.036820191 0.27480302 0.04324269
1600 0 -2.8931249 0.36718787 0.74943653 0.044424741
1650 0 -2.8858731 0.69688815 1.2623711 0.044835267
1700 0 -2.8755822 0.98073679 1.7977638 0.043907813
1750 0 -2.8722618 0.99796906 1.9978937 0.040932086
1800 0 -2.8731203 0.9972851 1.9960832 0.0397236
1850 0 -2.8733692 1.0063823 2.0084147 0.038402346
1900 0 -2.8743309 0.99390825 1.9917112 0.036653393
1950 0 -2.8747275 0.99296382 1.990551 0.03546065
2000 0 -2.8750021 0.99481655 1.9929497 0.034106229
2050 0 -2.8753234 0.9952595 1.9937091 0.032945475
2100 0 -2.8756779 0.99559778 1.9938914 0.031572327
2150 0 -2.8756378 1.0040013 2.0054123 0.030743908
2200 0 -2.8762771 0.99204187 1.9892722 0.029598229
2250 0 -2.8763962 0.99621035 1.9951999 0.028508126
2300 0 -2.8767096 0.99177935 1.9889303 0.027923296
2350 0 -2.8769679 0.99269877 1.9902617 0.026808323
2400 0 -2.8771042 0.99380193 1.9916833 0.025975215
2450 0 -2.8775424 0.99184579 1.97938 0.025568872
2500 0 -2.8771356 0.99828478 2.0052062 0.024736775
2550 0 -2.877267 1.002676 2.0046612 0.024421018
2600 0 -2.8773832 1.0034348 2.0036706 0.024252349
2650 0 -2.8774775 1.0022588 2.0041156 0.023860843
2700 0 -2.8775652 1.0037083 2.0040202 0.023507268
2750 0 -2.8776593 1.0024326 2.0044148 0.023198797
2800 0 -2.8777453 1.004064 2.0045537 0.02302249
2850 0 -2.8778605 1.002326 2.0041875 0.022701703
2900 0 -2.8779421 1.0039705 2.0044106 0.022501874
2950 0 -2.8780576 1.002205 2.004013 0.022286397
3000 0 -2.878144 1.0037936 2.0042112 0.022144639
3050 0 -2.878249 1.0024755 2.0043935 0.021868589
3100 0 -2.8783173 1.0046799 2.0055732 0.021796983
3150 0 -2.8784512 1.0027747 2.004865 0.021615784
3200 0 -2.878559 1.0041666 2.0046652 0.021479582
3250 0 -2.8786922 1.0022404 2.0040831 0.021320532
3300 0 -2.8787858 1.004096 2.004605 0.021189288
3350 0 -2.8789129 1.0026981 2.0047187 0.021127453
3400 0 -2.8790212 1.0043735 2.004995 0.021058606
3450 0 -2.879164 1.0027335 2.0047872 0.020974272
3500 0 -2.8792771 1.0044701 2.0051521 0.021070297
3550 0 -2.8794328 1.0028145 2.0049374 0.021192579
3600 0 -2.8795734 1.0042313 2.0047744 0.021292395
3650 0 -2.879737 1.0026704 2.0046899 0.02145695
3700 0 -2.8798799 1.004187 2.0046906 0.021670499
3750 0 -2.8800527 1.0025941 2.0045865 0.021931753
3800 0 -2.8801953 1.0043711 2.0050675 0.022267529
3850 0 -2.8803779 1.0028975 2.0049127 0.022644016
3900 0 -2.8805489 1.0042463 2.004839 0.02303546
3950 0 -2.8807459 1.0026018 2.0045822 0.023487163
4000 0 -2.8809206 1.0043211 2.0049365 0.024057735
4050 0 -2.8811306 1.0026751 2.0046604 0.024548779
4100 0 -2.8813175 1.0042501 2.004809 0.025223226
4150 0 -2.8815321 1.0026815 2.0047067 0.025879137
4200 0 -2.8817332 1.0041815 2.0047364 0.026433221
4250 0 -2.8819535 1.0027639 2.0047971 0.027074381
4300 0 -2.8821659 1.0043035 2.0049339 0.027735264
4350 0 -2.8824058 1.0026584 2.0046633 0.028227149
4400 0 -2.8826202 1.0043862 2.0050759 0.028797209
4450 0 -2.8828729 1.0026433 2.0046321 0.029235838
4500 0 -2.8830923 1.0043564 2.0050234 0.02975293
4550 0 -2.8833455 1.0028816 2.0049263 0.030073279
4600 0 -2.883583 1.0043256 2.0049185 0.030466167
4650 0 -2.8838564 1.0023697 2.0041961 0.030854459
4700 0 -2.8840754 1.0044469 2.0051821 0.031197341
4750 0 -2.8843436 1.002831 2.004918 0.031355133
4800 0 -2.8845917 1.0043757 2.0050274 0.031541443
4850 0 -2.8848671 1.0026986 2.0047156 0.031566784
4900 0 -2.8851161 1.0043141 2.0049762 0.031572733
4950 0 -2.8853964 1.002652 2.0046411 0.031331471
5000 0 -2.8856417 1.0044257 2.0051427 0.031202878
5050 0 -2.8859278 1.0027456 2.0047471 0.030775914
5100 0 -2.8861877 1.0042977 2.0049634 0.030441144
5150 0 -2.8864767 1.0027464 2.0047758 0.02978153
5200 0 -2.8867453 1.0043008 2.0049616 0.029063209
5250 0 -2.8870354 1.0027935 2.0048062 0.028245435
5300 0 -2.8873071 1.0043601 2.0050267 0.027521725
5350 0 -2.8876114 1.0026214 2.0046039 0.026634954
5400 0 -2.8878769 1.0044164 2.0051328 0.025778952
5450 0 -2.8881844 1.0027016 2.0046846 0.024723834
5500 0 -2.8884558 1.0044785 2.0052265 0.023706189
5550 0 -2.8887683 1.0027546 2.0048109 0.022459744
5600 0 -2.8890403 1.0045591 2.0053059 0.021203171
5650 0 -2.8893593 1.0027144 2.0047631 0.01970551
5700 0 -2.8896364 1.0046104 2.0053635 0.018169806
5750 0 -2.8899325 1.0032692 2.0055741 0.016385922
5800 0 -2.890229 1.0045078 2.0052321 0.014521168
5850 0 -2.8905415 1.0028424 2.0050024 0.012524183
5900 0 -2.8908238 1.0049628 2.0057692 0.010448481
5950 0 -2.8911634 1.0028239 2.0050924 0.0079933472
6000 0 -2.8914615 1.0049197 2.0055042 0.005512578
6050 0 -2.891809 1.0028681 2.0051886 0.0027066075
6100 0 -2.8921275 1.0052354 2.0059119 -1.5170443e-05
6150 0 -2.8925311 1.0024862 2.0049609 -0.002795792
6200 0 -2.8928601 1.0017098 2.0049899 -0.0052253341
6250 0 -2.8930615 1.0053803 2.0075809 -0.007194133
6300 0 -2.8935352 0.99905571 2.0016145 -0.0096001474
6350 0 -2.8937999 1.0039512 2.0027194 -0.011453741
6400 0 -2.8941238 1.0043347 2.0074111 -0.014196468
6450 0 -2.8946531 1.0056365 2.0061099 -0.017009608
6500 0 -2.8952396 1.0028504 2.005439 -0.019176641
6550 0 -2.8957887 1.0051549 2.0054964 -0.020783746
6600 0 -2.8963492 1.0033409 2.0059471 -0.021761418
6650 0 -2.8969158 1.0053128 2.0057702 -0.021968895
6700 0 -2.8976272 1.0027282 2.0057251 -0.022086108
6750 0 -2.8982968 1.0065938 2.0050641 -0.022568539
6800 0 -2.8989096 0.99666307 1.9917715 -0.023001041
6850 0 -2.8988567 1.0016996 2.00386 -0.023549106
6900 0 -2.899188 1.0018864 1.9973057 -0.023696051
6950 0 -2.8992845 1.0019601 2.0057552 -0.024164521
7000 0 -2.8996208 1.0047972 2.0009263 -0.024097154
7050 0 -2.9002588 0.99084281 1.9901195 -0.024350033
7100 0 -2.9004617 0.99703388 1.994421 -0.024490655
7150 0 -2.9011318 0.99392438 1.9936356 -0.024358695
7200 0 -2.9017299 0.99584554 1.9930404 -0.024166501
7250 0 -2.9022782 0.99338994 1.9925907 -0.023714272
7300 0 -2.9027424 0.99574804 1.992852 -0.023226666
7350 0 -2.9032209 0.99325942 1.9924179 -0.022676492
7400 0 -2.9036195 0.99587935 1.9930234 -0.022050714
7450 0 -2.9040602 0.99304372 1.9924225 -0.021334064
7500 0 -2.9044456 0.99574399 1.9929621 -0.020468113
7550 0 -2.9048928 0.99283125 1.9916196 -0.019745152
7600 0 -2.9052487 0.99613353 1.9929757 -0.01878099
7650 0 -2.9056838 0.9930926 1.9921128 -0.018076523
7700 0 -2.9060803 0.99531672 1.9923106 -0.017274375
7750 0 -2.9065194 0.99295164 1.9918983 -0.016776812
7800 0 -2.9069076 0.99581999 1.9928558 -0.016414512
7850 0 -2.9073591 0.9931813 1.9923196 -0.016151505
7900 0 -2.9077762 0.9952822 1.9923704 -0.015884543
7950 0 -2.9082184 0.99303267 1.9919 -0.015770026
8000 0 -2.9086243 0.99571188 1.9925882 -0.015502696
8050 0 -2.9090693 0.99302809 1.9920738 -0.015387613
8100 0 -2.909466 0.99566468 1.9926533 -0.015174688
8150 0 -2.9099165 0.9930803 1.9918066 -0.01527935
8200 0 -2.910309 0.99578925 1.9926599 -0.015137929
8250 0 -2.9107625 0.99296173 1.9917783 -0.01501993
8300 0 -2.9111717 0.99561737 1.9925441 -0.014840463
8350 0 -2.9116459 0.9930842 1.9920006 -0.014651227
8400 0 -2.9120664 0.99589068 1.9929837 -0.014404733
8450 0 -2.9125817 0.99327737 1.9923055 -0.014166223
8500 0 -2.9130964 0.995764 1.9929219 -0.013745204
8550 0 -2.913721 0.99359811 1.9926788 -0.013240653
8600 0 -2.9139305 1.0052621 2.0063975 -0.012763335
8650 0 -2.9144207 1.000171 2.0022216 -0.012252306
8700 0 -2.9149447 0.99704589 1.9923337 -0.011530912
8750 0 -2.9152104 0.99413522 1.9954113 -0.011224718
8800 0 -2.9154304 1.0041572 1.996481 -0.010486614
8850 0 -2.9159535 0.99229149 1.9896902 -0.010138691
8900 0 -2.9161096 0.99893906 1.9947765 -0.0098973816
8950 0 -2.9163734 0.99613603 1.9962343 -0.0097646929
9000 0 -2.916772 0.99746648 1.9948787 -0.009559373
9050 0 -2.9169999 1.0038678 2.0028722 -0.0099005156
9100 0 -2.9171948 1.0055979 2.005962 -0.010168465
9150 0 -2.9175792 1.0056384 2.0055831 -0.010545324
9200 0 -2.918316 1.003467 2.0019992 -0.011894619
9250 0 -2.918905 0.99416126 1.9897547 -0.012414724
9300 0 -2.9190059 1.0045845 2.0050386 -0.013476648
9350 0 -2.9193084 1.0043075 2.0035131 -0.014061442
9400 0 -2.9195274 1.0004097 2.0075884 -0.014669943
9450 0 -2.9196647 1.0078585 2.0083355 -0.014773122
9500 0 -2.920045 0.99720708 2.002851 -0.015372661
9550 0 -2.9201962 1.0038389 2.0030346 -0.015506301
9600 0 -2.9204398 1.0069753 2.0114581 -0.016339104
9650 0 -2.9208212 0.99631341 2.0030231 -0.016614789
9700 0 -2.9208843 1.0037705 2.0128886 -0.016882954
9750 0 -2.9214802 0.99373337 1.9924584 -0.016401176
9800 0 -2.9215167 1.0068503 1.9964267 -0.015715783
9850 0 -2.9215046 1.0005924 2.0050594 -0.015810235
9900 0 -2.921582 1.0110556 2.0046653 -0.015197287
9950 0 -2.9217936 1.0035561 2.0016688 -0.014919912
10000 0 -2.9218919 0.9986774 2.0059801 -0.014402484
10050 0 -2.922287 1.002836 1.9905929 -0.013111459
10100 0 -2.9222158 1.0001746 2.0012151 -0.012635659
10150 0 -2.9224668 0.9944203 1.9962869 -0.011523541
10200 0 -2.9226837 0.99831 1.9897002 -0.010231598
10250 0 -2.9226653 1.0031001 1.9970323 -0.0088422762
10300 0 -2.922597 1.0065743 2.0060393 -0.0074980789
10350 0 -2.9228195 0.99433146 2.0023639 -0.0066673288
10400 0 -2.9230978 0.99750867 1.9948447 -0.0043504002
10450 0 -2.9229895 0.99535681 2.0074668 -0.0028798679
10500 0 -2.9234529 0.99110704 1.9917133 -0.00045327289
10550 0 -2.9234805 0.99545445 1.9961 0.001710051
10600 0 -2.9235882 1.0054527 1.9957363 0.0046088264
10650 0 -2.9237144 0.99812094 1.9964942 0.0062983191
10700 0 -2.9240099 0.99145722 1.9888812 0.0082937382
10750 0 -2.923998 0.99396244 1.9992545 0.011675442
10800 0 -2.9241729 0.99706722 1.9980958 0.014976508
10850 0 -2.924221 1.0070608 2.0010354 0.018179217
10900 0 -2.9243888 0.99682932 2.0049201 0.021300775
10950 0 -2.9245898 0.9991085 2.0008019 0.02383127
11000 0 -2.9248079 0.99500439 1.9968747 0.02593884
11050 0 -2.9250582 1.0036919 1.9932297 0.029871699
11100 0 -2.9251939 0.99338379 1.9994486 0.032537644
11150 0 -2.9253686 1.0026492 1.9988011 0.035919671
11200 0 -2.9256832 0.99646255 1.9962014 0.038918266
11250 0 -2.9260443 0.99519652 1.9899849 0.042046322
11300 0 -2.9259773 1.0004947 2.0049386 0.044777218
11350 0 -2.9265098 0.99691435 1.9979313 0.049237927
11365 0 -2.9267488 0.99392914 1.9893654 0.049993204
Loop time of 2.07865 on 4 procs for 10000 steps with 800 atoms
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2.8790759758 -2.92679351312 -2.92674880547
Force two-norm initial, final = 3556.23 12.3258
Force max component initial, final = 2979.1 9.29982
Final line search alpha, max atom move = 3.45647e-05 0.000321445
Iterations, force evaluations = 10000 10065
Pair time (%) = 1.14782 (55.2193)
Neigh time (%) = 0.00358385 (0.172412)
Comm time (%) = 0.327161 (15.7391)
Outpt time (%) = 0.00532395 (0.256125)
Other time (%) = 0.594766 (28.613)
Nlocal: 200 ave 205 max 193 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 178.25 ave 182 max 174 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 1855.25 ave 1881 max 1810 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 7421
Ave neighs/atom = 9.27625
Neighbor list builds = 28
Dangerous builds = 0

97
regress/min/log.min.linux.4
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@ -1,97 +0,0 @@
thermo_modify format float %22.16g
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
thermo 100
run 1000
Memory usage per processor = 2.06131 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5.000000000000003 -2.461717005066061 0 2.532032994933942 5.019050890508955
100 3.278886388877869 -0.7431169835656971 0 2.531670797326075 15.91283242338088
200 3.304108155614702 -0.770002773686752 0 2.529975246733432 15.60265257745889
300 3.384022759512081 -0.848592112876043 0 2.531200618186648 15.18820325821745
400 3.391606335386342 -0.8569460127499905 0 2.530420814717119 15.38385255470058
500 3.313605249192515 -0.7793526398331005 0 2.530110602797923 15.83329554829931
600 3.388891509283207 -0.8521374176027908 0 2.532517977293812 15.16275872231016
700 3.212363247568808 -0.6764180715800802 0 2.531929721929266 16.31059174672587
800 3.30164965769371 -0.7657165604506752 0 2.531806035170918 15.63919769621543
900 3.462145385726328 -0.9260856989744829 0 2.531732005019688 14.7729646222292
1000 3.280307461900034 -0.744659361981205 0 2.531547715591454 15.83559687910055
Loop time of 0.150981 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.074358 (49.2498)
Neigh time (%) = 0.0259317 (17.1754)
Comm time (%) = 0.0378432 (25.0648)
Outpt time (%) = 0.000293195 (0.194193)
Other time (%) = 0.0125552 (8.31576)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 170.25 ave 176 max 167 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 1936.75 ave 1963 max 1896 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.74803 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.280307461900034 -0.744659361981205 0 2.531547715591454 15.83559687910055
1050 3.280307461900033 -2.819837129063572 0 0.4563699485090864 1.655394929592888
1100 3.280307461900033 -2.855498947211197 0 0.420708130361461 1.657155097577968
1150 3.280307461900033 -2.864669501007715 0 0.4115375765649429 1.704538802053384
1200 3.280307461900033 -2.868821260307581 0 0.4073858172650766 1.692208532293671
1250 3.280307461900033 -2.876498816721072 0 0.3997082608515861 1.69485318954625
1300 3.280307461900033 -2.877660562968008 0 0.3985465146046501 1.682138720151912
1350 3.280307461900033 -2.878937926575469 0 0.3972691509971895 1.671502430477356
1365 3.280307461900033 -2.879075975796061 0 0.3971311017765973 1.669229973578853
Loop time of 0.237022 on 4 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.744659361981 -2.87907436106 -2.8790759758
Force two-norm initial, final = 2006.88 0.477401
Force max component initial, final = 395.193 0.0879763
Final line search alpha, max atom move = 0.00334856 0.000294593
Iterations, force evaluations = 365 1437
Pair time (%) = 0.154196 (65.0556)
Neigh time (%) = 0.00975937 (4.1175)
Comm time (%) = 0.0475755 (20.0722)
Outpt time (%) = 0.000191867 (0.0809493)
Other time (%) = 0.0252992 (10.6738)
Nlocal: 200 ave 204 max 194 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 171.75 ave 173 max 170 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1762.75 ave 1797 max 1711 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 7051
Ave neighs/atom = 8.81375
Neighbor list builds = 78
Dangerous builds = 0

14
regress/regression.sh
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@ -1,14 +0,0 @@
#!/bin/bash
cd /code/lammps-atc/regress
./benchmark.py 4 12 min melt >& latest
fail=`grep -c FAIL latest`
addresses="rjones@sandia.gov jatempl@sandia.gov jzimmer@sandia.gov sjplimp@sandia.gov pscrozi@sandia.gov akohlmey@gmail.com"
subject="\"LAMMPS regression $fail tests failed\""
if [ $fail == 0 ] ; then
subject='"LAMMPS regression passed"'
fi
scp latest vikramarka.ca.sandia.gov:.
#echo $subject
#echo "mhmail $addresses -subject $subject < latest"
ssh vikramarka.ca.sandia.gov "mhmail $addresses -subject $subject < latest"