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fix the invoking issue

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This commit is contained in:
Wengen Ouyang
2021-12-01 04:56:46 +02:00
parent 8556b71949
commit 3bc36070a9
2 changed files with 21 additions and 26 deletions
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45
examples/sw/log.27Oct21.mos2_sw_mod.g++.1.before.change → examples/sw/log.27Oct21.mos2_sw_mod.g++.1
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@ -1,13 +1,13 @@
LAMMPS (27 Oct 2021)
LAMMPS (30 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# bilayer MoS2
# monolayer MoS2
units metal
boundary p p f
processors * * 1
atom_style full
read_data ./single_layer_MoS2.data
read_data single_layer_MoS2.data
Reading data file ...
triclinic box = (0.0000000 0.0000000 -100.00000) to (51.152320 44.299209 100.00000) with tilt (25.576160 0.0000000 0.0000000)
1 by 1 by 1 MPI processor grid
@ -20,21 +20,16 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.006 seconds
special bonds CPU = 0.001 seconds
read_data CPU = 0.005 seconds
variable mS equal 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
variable mMo equal 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
mass * ${mS}
mass * 32.065
mass 1 ${mMo}
mass 1 95.94
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
########################## Define potentials ################################
pair_style sw modify 1
pair_coeff * * tmd.sw Mo S S
Reading sw potential file tmd.sw with DATE: 2018-03-26
pair_style sw/mod
pair_coeff * * tmd.sw.mod Mo S S
Reading sw/mod potential file tmd.sw.mod with DATE: 2018-03-26
#########################################################################
### Simulation settings ####
@ -58,7 +53,7 @@ Neighbor list info ...
ghost atom cutoff = 5.158796
binsize = 2.579398, bins = 30 18 78
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
(1) pair sw/mod, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
@ -76,21 +71,21 @@ Step TotEng PotEng KinEng Temp
4000 -899.28397 -920.50737 21.223397 214.06955
4500 -899.28386 -919.79154 20.507685 206.85053
5000 -899.28077 -918.78947 19.508698 196.77425
Loop time of 3.13855 on 1 procs for 5000 steps with 768 atoms
Loop time of 2.88628 on 1 procs for 5000 steps with 768 atoms
Performance: 137.643 ns/day, 0.174 hours/ns, 1593.092 timesteps/s
Performance: 149.674 ns/day, 0.160 hours/ns, 1732.334 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0292 | 3.0292 | 3.0292 | 0.0 | 96.52
Bond | 0.0033211 | 0.0033211 | 0.0033211 | 0.0 | 0.11
Pair | 2.8297 | 2.8297 | 2.8297 | 0.0 | 98.04
Bond | 0.00028899 | 0.00028899 | 0.00028899 | 0.0 | 0.01
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.020003 | 0.020003 | 0.020003 | 0.0 | 0.64
Output | 0.0005136 | 0.0005136 | 0.0005136 | 0.0 | 0.02
Modify | 0.051294 | 0.051294 | 0.051294 | 0.0 | 1.63
Other | | 0.03422 | | | 1.09
Comm | 0.0095191 | 0.0095191 | 0.0095191 | 0.0 | 0.33
Output | 0.0002787 | 0.0002787 | 0.0002787 | 0.0 | 0.01
Modify | 0.034603 | 0.034603 | 0.034603 | 0.0 | 1.20
Other | | 0.01188 | | | 0.41
Nlocal: 768.000 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -106,4 +101,4 @@ Ave neighs/atom = 26.666667
Ave special neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:02

2
src/MANYBODY/pair_sw.h
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@ -61,7 +61,7 @@ class PairSW : public Pair {
void read_file(char *);
virtual void setup_params();
void twobody(Param *, double, double &, int, double &);
void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *,
virtual void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *,
int, double &);
};