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Stan bug fixes for fix reaxc/bonds/kk

This commit is contained in:
Steve Plimpton 2016-11-09 15:47:50 -07:00
parent bfea3dce7d
commit 9806da69f3
10 changed files with 15 additions and 197 deletions

4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="5 Nov 2016 version">
<META NAME="docnumber" CONTENT="9 Nov 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
5 Nov 2016 version :c,h4
9 Nov 2016 version :c,h4
Version info: :h4

2
doc/src/Section_commands.txt
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@ -886,6 +886,8 @@ KOKKOS, o = USER-OMP, t = OPT.
"body"_pair_body.html,
"bop"_pair_bop.html,
"born (go)"_pair_born.html,
"born/coul/dsf"_pair_born.html,
"born/coul/dsf/cs"_pair_born.html,
"born/coul/long (go)"_pair_born.html,
"born/coul/long/cs"_pair_born.html,
"born/coul/msm (o)"_pair_born.html,

10
doc/src/pair_born.txt
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@ -72,7 +72,6 @@ pair_style born/coul/dsf 0.1 10.0 12.0
pair_coeff * * 0.0 1.00 0.00 0.00 0.00
pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
[Description:]
The {born} style computes the Born-Mayer-Huggins or Tosi/Fumi
@ -101,9 +100,8 @@ term.
The {born/coul/wolf} style adds a Coulombic term as described for the
Wolf potential in the "coul/wolf"_pair_coul.html pair style.
The {born/coul/dsf} style computes the Coulomb contribution
with the damped shifted force model as in the
"coul/dsf"_pair_coul.html style.
The {born/coul/dsf} style computes the Coulomb contribution with the
damped shifted force model as in the "coul/dsf"_pair_coul.html style.
Style {born/coul/long/cs} is identical to {born/coul/long} except that
a term is added for the "core/shell model"_Section_howto.html#howto_25
@ -134,8 +132,8 @@ cutoff specified in the pair_style command is used.
For {born/coul/long}, {born/coul/wolf} and {born/coul/dsf} no
Coulombic cutoff can be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in
the pair_style command.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
:line

185
examples/coreshell/log.8Nov16.coreshell.dsf.2
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@ -1,185 +0,0 @@
LAMMPS (27 Oct 2016)
# Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 1 by 2 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
pair_style born/coul/dsf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 22
ghost atom cutoff = 22
binsize = 11 -> bins = 3 3 3
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
Memory usage per processor = 6.59457 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -635.80596 -675.46362 39.657659 1427 -21302.622 -675.46362 1.6320365 -677.09565 0 0 1.4528722e-14 2.747802e-15 13990.5
50 -634.54091 -666.58532 32.044415 1153.0529 -4531.3775 -668.37478 37.774715 -706.14949 0 1.7894556 9.6796061 2.2085323 13990.5
100 -632.30603 -662.37331 30.067272 1081.9095 -3494.2387 -664.52701 39.193627 -703.72064 0 2.1537086 11.074727 2.1546198 13990.5
150 -630.53361 -663.40981 32.876196 1182.9829 -73.383109 -665.83886 46.267578 -712.10644 0 2.4290532 11.741311 2.7510336 13990.5
200 -628.96388 -664.35527 35.391398 1273.4873 -1706.4631 -666.68771 41.799509 -708.48722 0 2.3324396 10.596222 3.0017211 13990.5
250 -627.71591 -662.45411 34.738199 1249.9833 -1256.9123 -665.05391 43.020328 -708.07424 0 2.5998001 10.583081 1.8375441 13990.5
300 -627.00338 -664.01808 37.014699 1331.8985 -1884.1512 -666.29225 40.78768 -707.07994 0 2.2741714 9.4246938 1.2451114 13990.5
350 -626.21003 -664.96799 38.757968 1394.6265 -1431.9753 -667.39487 41.866515 -709.26138 0 2.426873 10.31352 1.9959989 13990.5
400 -625.51909 -661.88115 36.362062 1308.4147 -366.8119 -664.48329 44.342045 -708.82533 0 2.60214 11.071369 2.1790546 13990.5
450 -624.9333 -661.08821 36.154909 1300.9607 -2315.3532 -663.62656 39.690513 -703.31708 0 2.5383564 10.013961 1.4015893 13990.5
500 -624.02542 -660.36457 36.339145 1307.59 374.84327 -663.00031 45.787267 -708.78758 0 2.6357437 10.67964 2.2503424 13990.5
Loop time of 5.89773 on 2 procs for 500 steps with 432 atoms
Performance: 14.650 ns/day, 1.638 hours/ns, 84.778 timesteps/s
99.9% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.2578 | 5.4112 | 5.5647 | 6.6 | 91.75
Bond | 0.0015583 | 0.0015992 | 0.0016401 | 0.1 | 0.03
Neigh | 0.076808 | 0.076815 | 0.076823 | 0.0 | 1.30
Comm | 0.23842 | 0.39185 | 0.54528 | 24.5 | 6.64
Output | 0.00029778 | 0.00038707 | 0.00047636 | 0.5 | 0.01
Modify | 0.0082664 | 0.0083008 | 0.0083351 | 0.0 | 0.14
Other | | 0.007544 | | | 0.13
Nlocal: 216 ave 220 max 212 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 7852 ave 7890 max 7814 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 148601 ave 149750 max 147452 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 297202
Ave neighs/atom = 687.968
Ave special neighs/atom = 1
Neighbor list builds = 21
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Memory usage per processor = 6.59743 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -624.02542 -660.36457 36.339145 1307.59 374.84327 -663.00031 45.787267 -708.78758 0 2.6357437 10.67964 2.2503424 13990.5
550 -624.01275 -659.6763 35.663547 1283.28 -408.77541 -662.43528 44.140494 -706.57577 0 2.7589824 11.231423 1.8578347 13990.5
600 -624.01608 -661.00741 36.991333 1331.0577 97.833921 -663.55203 45.177756 -708.72979 0 2.5446206 11.407616 1.9340498 13990.5
650 -624.01489 -661.39357 37.378678 1344.9955 -1635.0963 -663.98652 41.03269 -705.01921 0 2.5929525 9.7182838 1.8437992 13990.5
700 -624.01641 -660.60919 36.592785 1316.7168 274.84427 -663.34199 45.758937 -709.10093 0 2.7327992 11.40835 2.6926812 13990.5
750 -624.01423 -660.30947 36.295243 1306.0103 -424.48119 -662.95011 43.863553 -706.81366 0 2.6406337 11.369608 1.7919396 13990.5
800 -624.01561 -662.42457 38.408956 1382.068 -1601.0688 -664.8166 41.228621 -706.04522 0 2.3920376 10.379512 1.4876332 13990.5
850 -624.01051 -660.5341 36.523587 1314.2268 -1834.5447 -662.93225 40.927147 -703.8594 0 2.3981558 10.724301 2.0240776 13990.5
900 -624.01424 -662.4875 38.473259 1384.3818 -285.09099 -665.18917 44.16937 -709.35854 0 2.7016741 11.202878 2.9137876 13990.5
950 -624.01787 -661.88077 37.862897 1362.4192 294.61522 -664.50863 45.54898 -710.05761 0 2.6278644 12.347191 2.5194653 13990.5
1000 -624.01006 -658.82908 34.819022 1252.8915 1297.8621 -661.39405 48.235238 -709.62929 0 2.5649692 13.763173 2.6809836 13990.5
1050 -624.01237 -657.96252 33.950153 1221.627 -565.05956 -661.022 43.831206 -704.85321 0 3.059482 10.980185 1.5069363 13990.5
1100 -624.01221 -662.32641 38.314199 1378.6583 -1053.4531 -664.68928 42.37808 -707.06736 0 2.3628693 11.058878 2.310501 13990.5
1150 -624.01355 -663.31571 39.30216 1414.2081 -682.32516 -665.67212 42.824978 -708.4971 0 2.3564095 9.9617506 1.4794302 13990.5
1200 -624.01228 -660.54648 36.534208 1314.609 -1922.8104 -663.09623 40.35503 -703.45126 0 2.5497509 10.105408 1.5577027 13990.5
1250 -624.01453 -660.19988 36.18535 1302.056 1030.8826 -662.54352 47.329262 -709.87278 0 2.3436398 11.480691 2.3100697 13990.5
1300 -624.0174 -660.44812 36.430711 1310.8848 -592.37472 -663.42007 43.498393 -706.91846 0 2.9719516 10.517346 1.4566735 13990.5
1350 -624.02147 -662.7255 38.704027 1392.6855 328.82353 -665.26912 45.2889 -710.55802 0 2.5436194 11.071493 2.299515 13990.5
1400 -624.01155 -660.32249 36.310942 1306.5752 664.45071 -663.12835 46.391793 -709.52014 0 2.8058565 12.0411 2.0813357 13990.5
1450 -624.01128 -660.37598 36.364706 1308.5098 -954.57186 -662.9841 42.653305 -705.63741 0 2.6081222 10.498899 1.7930019 13990.5
1500 -624.01495 -658.96253 34.947585 1257.5176 14.253508 -661.8179 45.019135 -706.83704 0 2.8553699 10.911364 1.8897264 13990.5
Loop time of 11.7651 on 2 procs for 1000 steps with 432 atoms
Performance: 14.687 ns/day, 1.634 hours/ns, 84.997 timesteps/s
99.9% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.824 | 10.886 | 10.948 | 1.9 | 92.53
Bond | 0.0032091 | 0.0032401 | 0.0032711 | 0.1 | 0.03
Neigh | 0.16206 | 0.16206 | 0.16206 | 0.0 | 1.38
Comm | 0.62978 | 0.6916 | 0.75341 | 7.4 | 5.88
Output | 0.00071597 | 0.00087166 | 0.0010273 | 0.5 | 0.01
Modify | 0.0043559 | 0.0043788 | 0.0044017 | 0.0 | 0.04
Other | | 0.01691 | | | 0.14
Nlocal: 216 ave 224 max 208 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 7910 ave 7994 max 7826 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 148484 ave 151739 max 145228 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 296967
Ave neighs/atom = 687.424
Ave special neighs/atom = 1
Neighbor list builds = 46
Dangerous builds = 0
Total wall time: 0:00:17

0
examples/coreshell/log.8Nov16.coreshell.dsf.1 → examples/coreshell/log.9Nov16.coreshell.dsf.1
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3
src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
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@ -103,6 +103,7 @@ void FixReaxCBondsKokkos::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
((PairReaxCKokkos<LMPDeviceType>*) reaxc)->PackBondBuffer(k_buf,nbuf_local);
else
((PairReaxCKokkos<LMPHostType>*) reaxc)->PackBondBuffer(k_buf,nbuf_local);
buf[0] = nlocal;
// Receive information from buffer for output
RecvBuffer(buf, nbuf, nbuf_local, nlocal_tot, numbonds_max);
@ -110,6 +111,8 @@ void FixReaxCBondsKokkos::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
memory->destroy_kokkos(k_buf,buf);
}
/* ---------------------------------------------------------------------- */
double FixReaxCBondsKokkos::memory_usage()
{
double bytes;

2
src/KOKKOS/fix_reaxc_bonds_kokkos.h
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@ -32,7 +32,7 @@ class FixReaxCBondsKokkos : public FixReaxCBonds {
void init();
private:
double nbuf;
int nbuf;
void Output_ReaxC_Bonds(bigint, FILE *);
double memory_usage();
};

1
src/math_special.cpp
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@ -1,4 +1,3 @@
#include <math.h>
#include <stdint.h>
#include "math_special.h"

3
src/pair_born_coul_dsf.cpp
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@ -107,7 +107,8 @@ void PairBornCoulDSF::compute(int eflag, int vflag)
jlist = firstneigh[i];
jnum = numneigh[i];
// self coulombic energy
// self coulombic energy
if (eflag) {
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "5 Nov 2016"
#define LAMMPS_VERSION "9 Nov 2016"