diff --git a/examples/meam/msmeam/HGa.meam b/examples/meam/msmeam/HGa.meam new file mode 100644 index 0000000000..9f01501c16 --- /dev/null +++ b/examples/meam/msmeam/HGa.meam @@ -0,0 +1,30 @@ +bkgd_dyn = 1 +emb_lin_neg = 1 +augt1=0 +ialloy=1 +rc = 5.9 +#H +attrac(1,1)=0.460 +repuls(1,1)=0.460 +Cmin(1,1,1)=1.3 # PuMS +Cmax(1,1,1)= 2.80 +nn2(1,1)=1 +#Ga +rho0(2) = 0.6 +attrac(2,2)=0.097 +repuls(2,2)=0.097 +nn2(2,2)=1 +#HGa +attrac(1,2)=0.300 +repuls(1,2)=0.300 +lattce(1,2)=l12 +re(1,2)=3.19 +delta(1,2)=-0.48 +alpha(1,2)=6.6 +Cmin(1,1,2)=2.0 +Cmin(2,1,2)= 2.0 +Cmin(1,2,1)=2.0 +Cmin(2,2,1) = 1.4 +Cmin(1,2,2) = 1.4 +Cmin(1,1,2) = 1.4 +nn2(1,2)=1 diff --git a/examples/meam/msmeam/README.md b/examples/meam/msmeam/README.md new file mode 100644 index 0000000000..dbf569d4b3 --- /dev/null +++ b/examples/meam/msmeam/README.md @@ -0,0 +1,9 @@ +To run Baske's test, do + + lmp -in in.msmeam + +Then + + diff dump.msmeam dump.msmeam.bu + + diff --git a/examples/meam/msmeam/data.msmeam.bu b/examples/meam/msmeam/data.msmeam.bu new file mode 100644 index 0000000000..576a3c50de --- /dev/null +++ b/examples/meam/msmeam/data.msmeam.bu @@ -0,0 +1,25 @@ +LAMMPS data file via write_data, version 16 Feb 2016, timestep = 1 + +3 atoms +2 atom types + +-4.0000000000000000e+00 4.0000000000000000e+00 xlo xhi +-4.0000000000000000e+00 4.0000000000000000e+00 ylo yhi +-4.0000000000000000e+00 4.0000000000000000e+00 zlo zhi + +Masses + +1 1.0079 +2 69.723 + +Atoms # atomic + +1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0 +2 2 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0 +3 2 2.9999999999999999e-01 2.2999999999999998e+00 0.0000000000000000e+00 0 0 0 + +Velocities + +1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 +3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 diff --git a/examples/meam/msmeam/dump.msmeam.bu b/examples/meam/msmeam/dump.msmeam.bu new file mode 100644 index 0000000000..039f630073 --- /dev/null +++ b/examples/meam/msmeam/dump.msmeam.bu @@ -0,0 +1,24 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +3 +ITEM: BOX BOUNDS pp pp pp +-4 4 +-4 4 +-4 4 +ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] +1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0 +2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0 +3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0 +ITEM: TIMESTEP +1 +ITEM: NUMBER OF ATOMS +3 +ITEM: BOX BOUNDS pp pp pp +-4 4 +-4 4 +-4 4 +ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] +1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0 +2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0 +3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0 diff --git a/examples/meam/msmeam/in.msmeam b/examples/meam/msmeam/in.msmeam new file mode 100644 index 0000000000..82ffb89a13 --- /dev/null +++ b/examples/meam/msmeam/in.msmeam @@ -0,0 +1,31 @@ +echo both +log log.msmeam +# Test of MEAM potential for HGa + +# ------------------------ INITIALIZATION ---------------------------- +units metal +dimension 3 +boundary p p p +atom_style atomic +variable latparam equal 4.646 +variable ncell equal 3 + +# ----------------------- ATOM DEFINITION ---------------------------- +region box block -4 4 -4 4 -4 4 +create_box 2 box + +# + +include potential.mod +create_atoms 1 single 0 0 0 units box +create_atoms 2 single 2.2 0 0 units box +create_atoms 2 single 0.3 2.3 0 units box +# ---------- Define Settings --------------------- +variable teng equal "c_eatoms" +compute pot_energy all pe/atom +compute stress all stress/atom NULL +dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] +run 1 +write_data data.msmeam + +print "All done!" diff --git a/examples/meam/msmeam/library.msmeam b/examples/meam/msmeam/library.msmeam new file mode 100644 index 0000000000..9937eaee08 --- /dev/null +++ b/examples/meam/msmeam/library.msmeam @@ -0,0 +1,14 @@ +# DATE: 2018-09-22 UNITS: metal CONTRIBUTOR: Steve Valone, smv@lanl.gov CITATION: Baskes, PRB 1992; smv, sr, mib, JNM 2010 +# ms-meam data format May 2010 +# elt lat z ielement atwt +# alpha b0 b1 b2 b3 b1m b2m b3m alat esub asub +# - t0 t1 t2 t3 t1m t2m t3m rozero ibar +# NOTE: leading character cannot be a space + +'H' 'dim' 1.0 1 1.0079 +2.960 2.960 3.0 1.0 1.0 1.0 3.0 1.0 0.741 2.235 2.50 +1.0 0.44721 0.0 0.00 0.0 0.31623 0 6.70 0 + +'Ga4' 'fcc' 12.0 31 69.723 +4.42 4.80 3.10 6.00 0.00 0.0 0.0 0.5 4.247 2.897 0.97 +1.0 1.649 1.435 0.00 0.0 0.0 2.0 0.70 0 diff --git a/examples/meam/msmeam/log.msmeam.bu b/examples/meam/msmeam/log.msmeam.bu new file mode 100644 index 0000000000..8eac453c1e --- /dev/null +++ b/examples/meam/msmeam/log.msmeam.bu @@ -0,0 +1,107 @@ +# Test of MEAM potential for HGa + +# ------------------------ INITIALIZATION ---------------------------- +units metal +dimension 3 +boundary p p p +atom_style atomic +variable latparam equal 4.646 +variable ncell equal 3 + +# ----------------------- ATOM DEFINITION ---------------------------- +region box block -4 4 -4 4 -4 4 +create_box 2 box +Created orthogonal box = (-4 -4 -4) to (4 4 4) + 1 by 1 by 1 MPI processor grid + +# + +include potential.mod +# NOTE: This script can be modified for different pair styles +# See in.elastic for more info. + +variable Pu string H +print "potential chosen ${Pu}" +potential chosen H +# Choose potential +pair_style MSmeam +print "we just executed" +we just executed + +pair_coeff * * library.MSmeam ${Pu} Ga4 HGaMS.meam ${Pu} Ga4 +pair_coeff * * library.MSmeam H Ga4 HGaMS.meam ${Pu} Ga4 +pair_coeff * * library.MSmeam H Ga4 HGaMS.meam H Ga4 +Reading potential file library.MSmeam with DATE: 2018-09-22 +# Setup neighbor style +neighbor 1.0 nsq +neigh_modify once no every 1 delay 0 check yes + +# Setup minimization style +variable dmax equal 1.0e-2 +min_style cg +min_modify dmax ${dmax} line quadratic +min_modify dmax 0.01 line quadratic +compute eng all pe/atom +compute eatoms all reduce sum c_eng + +# Setup output +thermo 100 +thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms +thermo_modify norm yes +create_atoms 1 single 0 0 0 units box +Created 1 atoms +create_atoms 2 single 2.2 0 0 units box +Created 1 atoms +create_atoms 2 single 0.3 2.3 0 units box +Created 1 atoms +# ---------- Define Settings --------------------- +variable teng equal "c_eatoms" +compute pot_energy all pe/atom +compute stress all stress/atom NULL +dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] +run 1 +WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.9 + ghost atom cutoff = 6.9 +Memory usage per processor = 12.9295 Mbytes +Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume eatoms + 0 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079 + 1 0 15.433079 491354.68 838670.91 635393.13 0 80195.793 0 0 8 8 8 512 15.433079 +Loop time of 0.000172138 on 1 procs for 1 steps with 3 atoms + +Performance: 501.922 ns/day, 0.048 hours/ns, 5809.285 timesteps/s +81.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 | 0.0 | 38.92 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 1.11 +Output | 9.7036e-05 | 9.7036e-05 | 9.7036e-05 | 0.0 | 56.37 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 6.199e-06 | | | 3.60 + +Nlocal: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 78 ave 78 max 78 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7 ave 7 max 7 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 14 ave 14 max 14 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 14 +Ave neighs/atom = 4.66667 +Neighbor list builds = 0 +Dangerous builds = 0 +write_data data.msmeam + +print "All done!" +All done! +Total wall time: 0:00:00 + diff --git a/examples/meam/msmeam/msmeam.dump.bu b/examples/meam/msmeam/msmeam.dump.bu new file mode 100644 index 0000000000..039f630073 --- /dev/null +++ b/examples/meam/msmeam/msmeam.dump.bu @@ -0,0 +1,24 @@ +ITEM: TIMESTEP +0 +ITEM: NUMBER OF ATOMS +3 +ITEM: BOX BOUNDS pp pp pp +-4 4 +-4 4 +-4 4 +ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] +1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0 +2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0 +3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0 +ITEM: TIMESTEP +1 +ITEM: NUMBER OF ATOMS +3 +ITEM: BOX BOUNDS pp pp pp +-4 4 +-4 4 +-4 4 +ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] +1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0 +2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0 +3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0 diff --git a/examples/meam/msmeam/potential.mod b/examples/meam/msmeam/potential.mod new file mode 100644 index 0000000000..760cc93503 --- /dev/null +++ b/examples/meam/msmeam/potential.mod @@ -0,0 +1,25 @@ +# NOTE: This script can be modified for different pair styles +# See in.elastic for more info. + +variable Pu string H +print "potential chosen ${Pu}" +# Choose potential +pair_style meam/ms +print "we just executed" + +pair_coeff * * library.msmeam ${Pu} Ga4 HGa.meam ${Pu} Ga4 +# Setup neighbor style +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Setup minimization style +variable dmax equal 1.0e-2 +min_style cg +min_modify dmax ${dmax} line quadratic +compute eng all pe/atom +compute eatoms all reduce sum c_eng + +# Setup output +thermo 100 +thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms +thermo_modify norm yes