whitespace and output fixes.
This commit is contained in:
Axel Kohlmeyer
@ -1,19 +1,18 @@
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LAMMPS (5 May 2020)
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LAMMPS (2 Jun 2020)
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using 1 OpenMP thread(s) per MPI task
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units metal
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atom_style atomic
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read_data data.sigma5
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orthogonal box = (-90.272 -4.42719e-07 0) to (90.272 88.5438 17.5)
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orthogonal box = (-90.27200752837744 -4.427188724235731e-07 0.0) to (90.27200752837744 88.54377448471462 17.5)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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25600 atoms
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read_data CPU = 0.0209658 secs
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read_data CPU = 0.028 secs
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pair_style eam
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pair_coeff * * Ni_u3.eam
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Reading potential file Ni_u3.eam with DATE: 2007-06-11
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timestep 0.001
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Reading potential file Ni_u3.eam with DATE: 2007-06-11timestep 0.001
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fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
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fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
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@ -26,7 +25,7 @@ velocity all create 750 18527782
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#dump_modify save sort id
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run 1000
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fix orient/eco: cutoff=3.600000 norm_fac=30.012844 neighbors=18
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fix orient/eco: cutoff=3.6 norm_fac=30.012843706295556 neighbors=18
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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@ -57,20 +56,20 @@ Step Temp TotEng Press Volume f_eco
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800 664.91881 -109021.02 -62.347415 289323.84 -6.1930838
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900 704.83039 -108741.73 365.8898 289827.26 -9.8340949
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1000 734.71441 -108502.96 1119.6572 290190 -12.049805
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Loop time of 114.325 on 1 procs for 1000 steps with 25600 atoms
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Loop time of 116.807 on 1 procs for 1000 steps with 25600 atoms
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Performance: 0.756 ns/day, 31.757 hours/ns, 8.747 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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Performance: 0.740 ns/day, 32.446 hours/ns, 8.561 timesteps/s
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99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 27.174 | 27.174 | 27.174 | 0.0 | 23.77
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Neigh | 0.82192 | 0.82192 | 0.82192 | 0.0 | 0.72
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Comm | 0.12876 | 0.12876 | 0.12876 | 0.0 | 0.11
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Output | 0.00077987 | 0.00077987 | 0.00077987 | 0.0 | 0.00
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Modify | 86.114 | 86.114 | 86.114 | 0.0 | 75.32
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Other | | 0.0853 | | | 0.07
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Pair | 27.131 | 27.131 | 27.131 | 0.0 | 23.23
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Neigh | 0.83119 | 0.83119 | 0.83119 | 0.0 | 0.71
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Comm | 0.13038 | 0.13038 | 0.13038 | 0.0 | 0.11
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Output | 0.00079226 | 0.00079226 | 0.00079226 | 0.0 | 0.00
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Modify | 88.626 | 88.626 | 88.626 | 0.0 | 75.87
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Other | | 0.08717 | | | 0.07
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Nlocal: 25600 ave 25600 max 25600 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -88,4 +87,4 @@ Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:01:54
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Total wall time: 0:01:57
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@ -1,19 +1,18 @@
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LAMMPS (5 May 2020)
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LAMMPS (2 Jun 2020)
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using 1 OpenMP thread(s) per MPI task
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units metal
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atom_style atomic
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read_data data.sigma5
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orthogonal box = (-90.272 -4.42719e-07 0) to (90.272 88.5438 17.5)
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orthogonal box = (-90.27200752837744 -4.427188724235731e-07 0.0) to (90.27200752837744 88.54377448471462 17.5)
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4 by 1 by 1 MPI processor grid
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reading atoms ...
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25600 atoms
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read_data CPU = 0.0275698 secs
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read_data CPU = 0.329 secs
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pair_style eam
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pair_coeff * * Ni_u3.eam
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Reading potential file Ni_u3.eam with DATE: 2007-06-11
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timestep 0.001
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Reading potential file Ni_u3.eam with DATE: 2007-06-11timestep 0.001
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fix integrator all npt temp 750 750 0.1 iso 0 0 0.1
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fix eco all orient/eco 0.08 0.25 3.6 sigma5.ori
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@ -26,7 +25,7 @@ velocity all create 750 18527782
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#dump_modify save sort id
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run 1000
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fix orient/eco: cutoff=3.600000 norm_fac=30.012844 neighbors=18
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fix orient/eco: cutoff=3.6 norm_fac=30.012843706295556 neighbors=18
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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@ -57,20 +56,20 @@ Step Temp TotEng Press Volume f_eco
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800 664.86797 -109021.92 -52.316387 289313.22 -4.603192
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900 703.88411 -108742.88 329.87308 289838.93 -8.1835743
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1000 734.57012 -108504.44 1032.3825 290208.8 -9.5778417
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Loop time of 34.6285 on 4 procs for 1000 steps with 25600 atoms
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Loop time of 42.9059 on 4 procs for 1000 steps with 25600 atoms
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Performance: 2.495 ns/day, 9.619 hours/ns, 28.878 timesteps/s
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98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
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Performance: 2.014 ns/day, 11.918 hours/ns, 23.307 timesteps/s
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92.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 7.109 | 7.1216 | 7.136 | 0.4 | 20.57
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Neigh | 0.21069 | 0.21649 | 0.22302 | 1.1 | 0.63
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Comm | 0.15651 | 0.1704 | 0.17919 | 2.1 | 0.49
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Output | 0.0003221 | 0.00059247 | 0.0013802 | 0.0 | 0.00
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Modify | 27.057 | 27.074 | 27.084 | 0.2 | 78.18
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Other | | 0.04514 | | | 0.13
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Pair | 7.702 | 7.8512 | 8.0322 | 4.3 | 18.30
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Neigh | 0.21251 | 0.22612 | 0.24124 | 2.3 | 0.53
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Comm | 0.58286 | 0.84708 | 1.0824 | 19.5 | 1.97
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Output | 0.040286 | 0.048071 | 0.060272 | 3.8 | 0.11
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Modify | 33.411 | 33.509 | 33.606 | 1.3 | 78.10
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Other | | 0.4242 | | | 0.99
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Nlocal: 6400 ave 6429 max 6369 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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@ -88,4 +87,4 @@ Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:34
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Total wall time: 0:00:43
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@ -51,9 +51,9 @@ static const char cite_fix_orient_eco[] =
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" doi = {j.commatsci.2020.109774},\n"
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" url = {https://doi.org/10.1016/j.commatsci.2020.109774}\n"
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"}\n\n";
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#define FIX_ORIENT_ECO_MAX_NEIGH 24
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struct FixOrientECO::Nbr {
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public:
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int n; // # of neighbors
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@ -173,17 +173,12 @@ void FixOrientECO::init() {
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MPI_Comm_rank(world, &me);
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// compute normalization factor
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int neigh = get_norm();
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if (me == 0) {
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int neigh;
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get_norm(neigh);
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if (screen) {
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fprintf(screen, " fix orient/eco: cutoff=%f norm_fac=%f neighbors=%i\n", r_cut, norm_fac, neigh);
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}
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if (logfile) {
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fprintf(logfile, " fix orient/eco: cutoff=%f norm_fac=%f neighbors=%i\n", r_cut, norm_fac, neigh);
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}
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utils::logmesg(lmp,fmt::format(" fix orient/eco: cutoff={} norm_fac={} "
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"neighbors={}\n", r_cut, norm_fac, neigh));
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}
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inv_norm_fac = 1.0 / norm_fac;
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// check parameters
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@ -384,7 +379,7 @@ void FixOrientECO::post_force(int /* vflag */) {
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double sin_scalar_product; // sine of scalar product
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double gcos_scalar_product; // gradient weight function * cosine of scalar product
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double gsin_scalar_product; // gradient weight function * sine of scalar product
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// compute force only if synthetic
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// potential is not zero
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if (u_0 != 0.0) {
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@ -417,7 +412,7 @@ void FixOrientECO::post_force(int /* vflag */) {
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// loop over all neighbors of atom i
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for (j = 0; j < n; ++j) {
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idj = nbr[i].id[j];
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// compute force on atom i if it is close to boundary
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if ((nbr[idj].duchi != 0.0) || boundary_atom) {
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delta = &nbr[i].delta[j][0];
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@ -606,7 +601,7 @@ void FixOrientECO::get_reciprocal() {
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normalization factor
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------------------------------------------------------------------------- */
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void FixOrientECO::get_norm(int &neigh) {
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int FixOrientECO::get_norm() {
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// set up local variables
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double delta[3]; // relative position
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double squared_distance; // squared distance of atoms i and j
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@ -618,7 +613,7 @@ void FixOrientECO::get_norm(int &neigh) {
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int max_co = 4; // will produce wrong results for rcut > 3 * lattice constant
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neigh = 0; // count number of neighbors used
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int neigh = 0; // count number of neighbors used
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// loop over ideal lattice positions
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int i, k, idx[3];
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@ -656,6 +651,7 @@ void FixOrientECO::get_norm(int &neigh) {
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for (k = 0; k < 3; ++k) {
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norm_fac -= reesum[k] * reesum[k] + imesum[k] * imesum[k];
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}
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return neigh;
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}
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@ -41,7 +41,7 @@ class FixOrientECO : public Fix {
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private:
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struct Nbr; // private struct for managing precomputed terms
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int me; // this processors rank
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int nmax; // maximal # of owned + ghost atoms on this processor
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int ilevel_respa; // used for RESPA integrator only
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@ -70,7 +70,7 @@ class FixOrientECO : public Fix {
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class NeighList *list; // LAMMPS' neighbor list
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void get_reciprocal(); // calculate reciprocal lattice vectors
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void get_norm(int &); // compute normalization factor
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int get_norm(); // compute normalization factor
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};
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}
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