forked from lijiext/lammps
2nd try on LATTE error returns, plus a couple minor doc edits
This commit is contained in:
Steven J. Plimpton
parent
9cf99ef479
commit
c399b75dec
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@ -978,6 +978,7 @@ KOKKOS, o = USER-OMP, t = OPT.
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"lj/cut/coul/long (gikot)"_pair_lj.html,
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"lj/cut/coul/long/cs"_pair_lj.html,
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"lj/cut/coul/msm (go)"_pair_lj.html,
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"lj/cut/coul/wolf (o)"_pair_lj.html,
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"lj/cut/dipole/cut (go)"_pair_dipole.html,
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"lj/cut/dipole/long"_pair_dipole.html,
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"lj/cut/tip4p/cut (o)"_pair_lj.html,
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@ -1011,7 +1012,7 @@ KOKKOS, o = USER-OMP, t = OPT.
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"reax"_pair_reax.html,
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"rebo (oi)"_pair_airebo.html,
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"resquared (go)"_pair_resquared.html,
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"snap"_pair_snap.html,
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"snap (k)"_pair_snap.html,
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"soft (go)"_pair_soft.html,
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"sw (giko)"_pair_sw.html,
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"table (gko)"_pair_table.html,
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@ -1,78 +0,0 @@
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LAMMPS (23 Oct 2015)
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# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
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# input for relaxed vacancy formation energy at constant pressure
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echo screen
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Lattice spacing in x,y,z = 6.23812 6.23812 6.23812
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Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906)
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1 by 1 by 1 MPI processor grid
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Created 250 atoms
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Deleted 1 atoms, new total = 249
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Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 13.1712
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ghost atom cutoff = 13.1712
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binsize = 6.58562 -> bins = 5 5 5
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Memory usage per processor = 4.66978 Mbytes
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Step Volume Temp PotEng TotEng Press
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0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
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10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
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20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
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30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
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40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
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50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
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60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
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70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
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80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
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90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
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100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
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110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
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120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
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130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
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139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
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Loop time of 4.33109 on 1 procs for 139 steps with 249 atoms
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92.4% CPU use with 1 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-73.9945109564 -74.0063705487 -74.0063705557
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Force two-norm initial, final = 0.0366227 8.09081e-05
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Force max component initial, final = 0.00730948 8.05242e-06
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Final line search alpha, max atom move = 1 8.05242e-06
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Iterations, force evaluations = 139 139
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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 | 4.3064 | 4.3064 | 4.3064 | 0.0 | 99.43
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Neigh | 0.019113 | 0.019113 | 0.019113 | 0.0 | 0.44
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Comm | 0.0017624 | 0.0017624 | 0.0017624 | 0.0 | 0.04
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Output | 0.00084376 | 0.00084376 | 0.00084376 | 0.0 | 0.02
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.00297 | | | 0.07
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Nlocal: 249 ave 249 max 249 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1479 ave 1479 max 1479 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 7936 ave 7936 max 7936 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 15872 ave 15872 max 15872 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 15872
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Ave neighs/atom = 63.743
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Neighbor list builds = 4
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Dangerous builds = 0
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number of atoms = 249
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atomic volume (a.u.) = 121.863
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total energy (ry/atom) = -0.594428679162064
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pressure (gpa) = -1.15783109519801
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249 121.863 -148.012741111354 -1.15783109519801
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121.863 -0.594428679162064 -1.15783109519801
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Total wall time: 0:00:04
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@ -12,7 +12,7 @@ CONTROL{
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xControl= 1
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BASISTYPE= NONORTHO
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COORDSFILE= "./coords.dat"
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PARAMPATH= "/home/user/LATTE/TBparam"
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PARAMPATH= "./TBparam"
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KBT= 0.0
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ENTROPYKIND= 1
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PPOTON= 1
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@ -38,7 +38,7 @@ extern "C" {
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void latte(int *, int *, double *, int *, int *,
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double *, double *, double *, double *,
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double *, double *, double *, int*,
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double *, double *, double *, double * );
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double *, double *, double *, double *, bool *);
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}
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#define INVOKED_PERATOM 8
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@ -267,7 +267,7 @@ void FixLatte::post_force(int vflag)
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flags[1] = coulombflag; // 1 for LAMMPS computes Coulombics, 0 for LATTE
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flags[2] = eflag_atom; // 1 to return per-atom energies, 0 for no
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flags[3] = vflag_global && thermo_virial; // 1 to return global/per-atom
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flags[4] = vflag_atom && thermo_virial; // virial, 0 for no
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flags[4] = vflag_atom && thermo_virial; // virial, 0 for no
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flags[5] = neighflag; // 1 to pass neighbor list to LATTE, 0 for no
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// setup LATTE arguments
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@ -279,16 +279,17 @@ void FixLatte::post_force(int vflag)
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double *mass = &atom->mass[1];
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double *boxlo = domain->boxlo;
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double *boxhi = domain->boxhi;
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double *forces;
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bool latteerror = 0;
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if (coulomb) forces = &flatte[0][0];
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else forces = &atom->f[0][0];
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int maxiter = -1;
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latte(flags,&natoms,coords,type,&ntypes,mass,boxlo,boxhi,&domain->xy,
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&domain->xz,&domain->yz,
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forces,&maxiter,&latte_energy,&atom->v[0][0],&update->dt,virial);
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&domain->xz,&domain->yz,forces,&maxiter,&latte_energy,
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&atom->v[0][0],&update->dt,virial,&latteerror);
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if (latteerror) error->all(FLERR,"Internal LATTE problem");
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// sum LATTE forces to LAMMPS forces
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// e.g. LAMMPS may compute Coulombics at some point
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@ -350,7 +350,6 @@ void Fix::v_tally(int n, int *list, double total, double *v)
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void Fix::v_tally(int i, double *v)
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{
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if (vflag_global) {
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virial[0] += v[0];
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virial[1] += v[1];
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@ -384,7 +383,6 @@ void Fix::v_tally(int i, double *v)
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void Fix::v_tally(int n, int i, double vn)
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{
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if (vflag_global)
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virial[n] += vn;
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