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whitespace and output fixes.

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This commit is contained in:
Axel Kohlmeyer
2020-06-06 11:10:32 -04:00
parent 92012ef047
commit d343d2beb1
4 changed files with 43 additions and 49 deletions
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31
examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.1
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@ -1,19 +1,18 @@
LAMMPS (5 May 2020)
LAMMPS (2 Jun 2020)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
read_data data.sigma5
orthogonal box = (-90.272 -4.42719e-07 0) to (90.272 88.5438 17.5)
orthogonal box = (-90.27200752837744 -4.427188724235731e-07 0.0) to (90.27200752837744 88.54377448471462 17.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
25600 atoms
read_data CPU = 0.0209658 secs
read_data CPU = 0.028 secs
pair_style eam
pair_coeff * * Ni_u3.eam
Reading potential file Ni_u3.eam with DATE: 2007-06-11
timestep 0.001
Reading potential file Ni_u3.eam with DATE: 2007-06-11timestep 0.001
fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
@ -26,7 +25,7 @@ velocity all create 750 18527782
#dump_modify save sort id
run 1000
fix orient/eco: cutoff=3.600000 norm_fac=30.012844 neighbors=18
fix orient/eco: cutoff=3.6 norm_fac=30.012843706295556 neighbors=18
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -57,20 +56,20 @@ Step Temp TotEng Press Volume f_eco
800 664.91881 -109021.02 -62.347415 289323.84 -6.1930838
900 704.83039 -108741.73 365.8898 289827.26 -9.8340949
1000 734.71441 -108502.96 1119.6572 290190 -12.049805
Loop time of 114.325 on 1 procs for 1000 steps with 25600 atoms
Loop time of 116.807 on 1 procs for 1000 steps with 25600 atoms
Performance: 0.756 ns/day, 31.757 hours/ns, 8.747 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.740 ns/day, 32.446 hours/ns, 8.561 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 | 27.174 | 27.174 | 27.174 | 0.0 | 23.77
Neigh | 0.82192 | 0.82192 | 0.82192 | 0.0 | 0.72
Comm | 0.12876 | 0.12876 | 0.12876 | 0.0 | 0.11
Output | 0.00077987 | 0.00077987 | 0.00077987 | 0.0 | 0.00
Modify | 86.114 | 86.114 | 86.114 | 0.0 | 75.32
Other | | 0.0853 | | | 0.07
Pair | 27.131 | 27.131 | 27.131 | 0.0 | 23.23
Neigh | 0.83119 | 0.83119 | 0.83119 | 0.0 | 0.71
Comm | 0.13038 | 0.13038 | 0.13038 | 0.0 | 0.11
Output | 0.00079226 | 0.00079226 | 0.00079226 | 0.0 | 0.00
Modify | 88.626 | 88.626 | 88.626 | 0.0 | 75.87
Other | | 0.08717 | | | 0.07
Nlocal: 25600 ave 25600 max 25600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -88,4 +87,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:54
Total wall time: 0:01:57

31
examples/USER/misc/orient_eco/log.2Jun2020.orent_eco.g++.4
View File

@ -1,19 +1,18 @@
LAMMPS (5 May 2020)
LAMMPS (2 Jun 2020)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
read_data data.sigma5
orthogonal box = (-90.272 -4.42719e-07 0) to (90.272 88.5438 17.5)
orthogonal box = (-90.27200752837744 -4.427188724235731e-07 0.0) to (90.27200752837744 88.54377448471462 17.5)
4 by 1 by 1 MPI processor grid
reading atoms ...
25600 atoms
read_data CPU = 0.0275698 secs
read_data CPU = 0.329 secs
pair_style eam
pair_coeff * * Ni_u3.eam
Reading potential file Ni_u3.eam with DATE: 2007-06-11
timestep 0.001
Reading potential file Ni_u3.eam with DATE: 2007-06-11timestep 0.001
fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
@ -26,7 +25,7 @@ velocity all create 750 18527782
#dump_modify save sort id
run 1000
fix orient/eco: cutoff=3.600000 norm_fac=30.012844 neighbors=18
fix orient/eco: cutoff=3.6 norm_fac=30.012843706295556 neighbors=18
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -57,20 +56,20 @@ Step Temp TotEng Press Volume f_eco
800 664.86797 -109021.92 -52.316387 289313.22 -4.603192
900 703.88411 -108742.88 329.87308 289838.93 -8.1835743
1000 734.57012 -108504.44 1032.3825 290208.8 -9.5778417
Loop time of 34.6285 on 4 procs for 1000 steps with 25600 atoms
Loop time of 42.9059 on 4 procs for 1000 steps with 25600 atoms
Performance: 2.495 ns/day, 9.619 hours/ns, 28.878 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 2.014 ns/day, 11.918 hours/ns, 23.307 timesteps/s
92.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.109 | 7.1216 | 7.136 | 0.4 | 20.57
Neigh | 0.21069 | 0.21649 | 0.22302 | 1.1 | 0.63
Comm | 0.15651 | 0.1704 | 0.17919 | 2.1 | 0.49
Output | 0.0003221 | 0.00059247 | 0.0013802 | 0.0 | 0.00
Modify | 27.057 | 27.074 | 27.084 | 0.2 | 78.18
Other | | 0.04514 | | | 0.13
Pair | 7.702 | 7.8512 | 8.0322 | 4.3 | 18.30
Neigh | 0.21251 | 0.22612 | 0.24124 | 2.3 | 0.53
Comm | 0.58286 | 0.84708 | 1.0824 | 19.5 | 1.97
Output | 0.040286 | 0.048071 | 0.060272 | 3.8 | 0.11
Modify | 33.411 | 33.509 | 33.606 | 1.3 | 78.10
Other | | 0.4242 | | | 0.99
Nlocal: 6400 ave 6429 max 6369 min
Histogram: 1 1 0 0 0 0 0 0 0 2
@ -88,4 +87,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:34
Total wall time: 0:00:43

16
src/USER-MISC/fix_orient_eco.cpp
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@ -173,15 +173,10 @@ void FixOrientECO::init() {
MPI_Comm_rank(world, &me);
// compute normalization factor
int neigh = get_norm();
if (me == 0) {
int neigh;
get_norm(neigh);
if (screen) {
fprintf(screen, " fix orient/eco: cutoff=%f norm_fac=%f neighbors=%i\n", r_cut, norm_fac, neigh);
}
if (logfile) {
fprintf(logfile, " fix orient/eco: cutoff=%f norm_fac=%f neighbors=%i\n", r_cut, norm_fac, neigh);
}
utils::logmesg(lmp,fmt::format(" fix orient/eco: cutoff={} norm_fac={} "
"neighbors={}\n", r_cut, norm_fac, neigh));
}
inv_norm_fac = 1.0 / norm_fac;
@ -606,7 +601,7 @@ void FixOrientECO::get_reciprocal() {
normalization factor
------------------------------------------------------------------------- */
void FixOrientECO::get_norm(int &neigh) {
int FixOrientECO::get_norm() {
// set up local variables
double delta[3]; // relative position
double squared_distance; // squared distance of atoms i and j
@ -618,7 +613,7 @@ void FixOrientECO::get_norm(int &neigh) {
int max_co = 4; // will produce wrong results for rcut > 3 * lattice constant
neigh = 0; // count number of neighbors used
int neigh = 0; // count number of neighbors used
// loop over ideal lattice positions
int i, k, idx[3];
@ -656,6 +651,7 @@ void FixOrientECO::get_norm(int &neigh) {
for (k = 0; k < 3; ++k) {
norm_fac -= reesum[k] * reesum[k] + imesum[k] * imesum[k];
}
return neigh;
}

2
src/USER-MISC/fix_orient_eco.h
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@ -70,7 +70,7 @@ class FixOrientECO : public Fix {
class NeighList *list; // LAMMPS' neighbor list
void get_reciprocal(); // calculate reciprocal lattice vectors
void get_norm(int &); // compute normalization factor
int get_norm(); // compute normalization factor
};
}