Commit e38f9706 authored by Aidan Thompson's avatar Aidan Thompson
Browse files

Extended to handle gradgradflag 0/1 options

parent 0d570f55

examples/mliap/in.mliap.quadratic.compute

+20 −10
Original line number Diff line number Diff line
@@ -67,13 +67,6 @@ compute vbsum all reduce sum c_vb[*] 
# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector

variable	db_2_100 equal c_db[2][100]



# set up compute snap generating global array



compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector



thermo 		100



# test output:   1: total potential energy

#                2: xy component of stress tensor

#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
@@ -81,15 +74,32 @@ thermo 100 
#                5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)

#

#                followed by 5 counterparts from compute snap

thermo 		100



# run compute mliap with gradgradflag = 1



compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector



thermo_style	custom &

		pe            pxy            c_bsum2[20]   c_vbsum[220]    v_db_2_100 &

		c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] 

thermo_modify 	norm no



# dump 		mydump_db all custom 1000 dump_db id c_db[*]

# dump_modify 	mydump_db sort id

run             ${nsteps}



uncompute	snap

unfix		snap



# run compute mliap with gradgradflag = 0



# Run MD

compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector



thermo_style	custom &

		pe            pxy            c_bsum2[20]   c_vbsum[220]    v_db_2_100 &

		c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] 

thermo_modify 	norm no



run             ${nsteps}

examples/mliap/in.mliap.snap.compute

+18 −8
Original line number Diff line number Diff line
@@ -67,11 +67,6 @@ compute vbsum all reduce sum c_vb[*] 
# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector

variable	db_2_25 equal c_db[2][25]



# set up compute snap generating global array



compute   	snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector



thermo 		100



# test output:   1: total potential energy
@@ -82,14 +77,29 @@ thermo 100 
#

#                followed by 5 counterparts from compute snap



# run compute mliap with gradgradflag = 1



compute   	snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector



thermo_style	custom &

		pe            pxy            c_bsum2[1]   c_vbsum[55]    v_db_2_25 &

		c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12] 

thermo_modify 	norm no



# dump 		mydump_db all custom 1000 dump_db id c_db[*]

# dump_modify 	mydump_db sort id

run             ${nsteps}



uncompute	snap

unfix		snap



# run compute mliap with gradgradflag = 0



# Run MD

compute   	snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 0

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector



thermo_style	custom &

		pe            pxy            c_bsum2[1]   c_vbsum[55]    v_db_2_25 &

		c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12] 

thermo_modify 	norm no



run             ${nsteps}

examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.1

+107 −25
Original line number Diff line number Diff line 
LAMMPS (15 Jun 2020)

LAMMPS (30 Jun 2020)

# Demonstrate MLIAP quadratic compute



# initialize simulation
@@ -28,7 +28,7 @@ region box block 0 1 0 ${ny} 0 ${nz} 
region		box block 0 1 0 1 0 ${nz}

region		box block 0 1 0 1 0 1

create_box	2 box

Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)

Created orthogonal box = (0 0 0) to (2 2 2)

  1 by 1 by 1 MPI processor grid

create_atoms	2 box

Created 2 atoms
@@ -99,9 +99,18 @@ compute vbsum all reduce sum c_vb[*] 
# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector

variable	db_2_100 equal c_db[2][100]



# set up compute snap generating global array

# test output:   1: total potential energy

#                2: xy component of stress tensor

#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2)

#                4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)

#                5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)

#

#                followed by 5 counterparts from compute snap

thermo 		100



# run compute mliap with gradgradflag = 1



compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21

compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1

SNAP keyword rcutfac 1.0 

SNAP keyword twojmax 2 

SNAP keyword nelems 2
@@ -112,25 +121,97 @@ SNAP keyword rfac0 0.99363 
SNAP keyword rmin0 0 

SNAP keyword bzeroflag 0 

SNAP keyword switchflag 0 

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector



thermo 		100



# test output:   1: total potential energy

#                2: xy component of stress tensor

#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2)

#                4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)

#                5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)

#

#                followed by 5 counterparts from compute snap

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector



thermo_style	custom 		pe            pxy            c_bsum2[20]   c_vbsum[220]    v_db_2_100 		c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]

thermo_modify 	norm no



# dump 		mydump_db all custom 1000 dump_db id c_db[*]

# dump_modify 	mydump_db sort id

run             ${nsteps}

run             0

Neighbor list info ...

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 6.8

  ghost atom cutoff = 6.8

  binsize = 3.4, bins = 1 1 1

  5 neighbor lists, perpetual/occasional/extra = 1 4 0

  (1) pair zbl, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/3d/newton

      bin: standard

  (2) compute sna/atom, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

  (3) compute snav/atom, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

  (4) compute snad/atom, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

  (5) compute mliap, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 22.45 | 22.45 | 22.45 Mbytes

PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] 

   322.86952    1505558.1 4.2492771e+08     -4952473     28484035    322.86952    1505558.1 4.2492771e+08     -4952473     28484035 

Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms



200.0% CPU use with 1 MPI tasks x no OpenMP threads



# Run MD

MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0          | 0          | 0          |   0.0 |  0.00

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 0          | 0          | 0          |   0.0 |  0.00

Output  | 0          | 0          | 0          |   0.0 |  0.00

Modify  | 0          | 0          | 0          |   0.0 |  0.00

Other   |            | 1e-06      |            |       |100.00



Nlocal:    2.0 ave 2.0 max 2.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    853.0 ave 853.0 max 853.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    330.0 ave 330.0 max 330.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

FullNghs:  660.0 ave 660.0 max 660.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 660

Ave neighs/atom = 330.0

Neighbor list builds = 0

Dangerous builds = 0



uncompute	snap

unfix		snap



# run compute mliap with gradgradflag = 0



compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0

SNAP keyword rcutfac 1.0 

SNAP keyword twojmax 2 

SNAP keyword nelems 2 

SNAP keyword elems A 

SNAP keyword radelems 2.3 

SNAP keyword welems 1.0 

SNAP keyword rfac0 0.99363 

SNAP keyword rmin0 0 

SNAP keyword bzeroflag 0 

SNAP keyword switchflag 0 

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector



thermo_style	custom 		pe            pxy            c_bsum2[20]   c_vbsum[220]    v_db_2_100 		c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]

WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:694)

thermo_modify 	norm no



run             ${nsteps}

run             0
@@ -166,12 +247,12 @@ Neighbor list info ... 
      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 22.45 | 22.45 | 22.45 Mbytes

Per MPI rank memory allocation (min/avg/max) = 70.2 | 70.2 | 70.2 Mbytes

PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] 

   322.86952    1505558.1 4.2492771e+08     -4952473     28484035    322.86952    1505558.1 4.2492771e+08     -4952473     28484035 

Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms



100.0% CPU use with 1 MPI tasks x no OpenMP threads

200.0% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total
@@ -183,17 +264,18 @@ Output | 0 | 0 | 0 | 0.0 | 0.00 
Modify  | 0          | 0          | 0          |   0.0 |  0.00

Other   |            | 1e-06      |            |       |100.00



Nlocal:    2 ave 2 max 2 min

Nlocal:    2.0 ave 2.0 max 2.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    853 ave 853 max 853 min

Nghost:    853.0 ave 853.0 max 853.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    330 ave 330 max 330 min

Neighs:    330.0 ave 330.0 max 330.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

FullNghs:  660 ave 660 max 660 min

FullNghs:  660.0 ave 660.0 max 660.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 660

Ave neighs/atom = 330

Ave neighs/atom = 330.0

Neighbor list builds = 0

Dangerous builds = 0



Total wall time: 0:00:00

examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.4

+109 −26
Original line number Diff line number Diff line 
LAMMPS (15 Jun 2020)

LAMMPS (30 Jun 2020)

# Demonstrate MLIAP quadratic compute



# initialize simulation
@@ -28,7 +28,7 @@ region box block 0 1 0 ${ny} 0 ${nz} 
region		box block 0 1 0 1 0 ${nz}

region		box block 0 1 0 1 0 1

create_box	2 box

Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)

Created orthogonal box = (0 0 0) to (2 2 2)

  1 by 2 by 2 MPI processor grid

create_atoms	2 box

Created 2 atoms
@@ -99,9 +99,18 @@ compute vbsum all reduce sum c_vb[*] 
# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector

variable	db_2_100 equal c_db[2][100]



# set up compute snap generating global array

# test output:   1: total potential energy

#                2: xy component of stress tensor

#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2)

#                4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)

#                5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)

#

#                followed by 5 counterparts from compute snap

thermo 		100



# run compute mliap with gradgradflag = 1



compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21

compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1

SNAP keyword rcutfac 1.0 

SNAP keyword twojmax 2 

SNAP keyword nelems 2
@@ -112,25 +121,98 @@ SNAP keyword rfac0 0.99363 
SNAP keyword rmin0 0 

SNAP keyword bzeroflag 0 

SNAP keyword switchflag 0 

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector



thermo 		100



# test output:   1: total potential energy

#                2: xy component of stress tensor

#                3: Sum(0.5*(B_{222}^i)^2, all i of type 2)

#                4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)

#                5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)

#

#                followed by 5 counterparts from compute snap

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector



thermo_style	custom 		pe            pxy            c_bsum2[20]   c_vbsum[220]    v_db_2_100 		c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]

thermo_modify 	norm no



# dump 		mydump_db all custom 1000 dump_db id c_db[*]

# dump_modify 	mydump_db sort id

run             ${nsteps}

run             0

Neighbor list info ...

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 6.8

  ghost atom cutoff = 6.8

  binsize = 3.4, bins = 1 1 1

  5 neighbor lists, perpetual/occasional/extra = 1 4 0

  (1) pair zbl, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/3d/newton

      bin: standard

  (2) compute sna/atom, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

  (3) compute snav/atom, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

  (4) compute snad/atom, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

  (5) compute mliap, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)

Per MPI rank memory allocation (min/avg/max) = 22.18 | 22.18 | 22.18 Mbytes

PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] 

   322.86952    1505558.1 4.2492771e+08     -4952473     28484035    322.86952    1505558.1 4.2492771e+08     -4952473     28484035 

Loop time of 3.5e-06 on 4 procs for 0 steps with 2 atoms



92.9% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0          | 0          | 0          |   0.0 |  0.00

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 0          | 0          | 0          |   0.0 |  0.00

Output  | 0          | 0          | 0          |   0.0 |  0.00

Modify  | 0          | 0          | 0          |   0.0 |  0.00

Other   |            | 3.5e-06    |            |       |100.00



Nlocal:    0.5 ave 1.0 max 0.0 min

Histogram: 2 0 0 0 0 0 0 0 0 2

Nghost:    734.5 ave 735.0 max 734.0 min

Histogram: 2 0 0 0 0 0 0 0 0 2

Neighs:    82.5 ave 177.0 max 0.0 min

Histogram: 2 0 0 0 0 0 0 0 1 1

FullNghs:  165.0 ave 330.0 max 0.0 min

Histogram: 2 0 0 0 0 0 0 0 0 2



Total # of neighbors = 660

Ave neighs/atom = 330.0

Neighbor list builds = 0

Dangerous builds = 0



# Run MD

uncompute	snap

unfix		snap



# run compute mliap with gradgradflag = 0



compute   	snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0

SNAP keyword rcutfac 1.0 

SNAP keyword twojmax 2 

SNAP keyword nelems 2 

SNAP keyword elems A 

SNAP keyword radelems 2.3 

SNAP keyword welems 1.0 

SNAP keyword rfac0 0.99363 

SNAP keyword rmin0 0 

SNAP keyword bzeroflag 0 

SNAP keyword switchflag 0 

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector



thermo_style	custom 		pe            pxy            c_bsum2[20]   c_vbsum[220]    v_db_2_100 		c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]

WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:694)

thermo_modify 	norm no



run             ${nsteps}

run             0
@@ -167,10 +249,10 @@ Neighbor list info ... 
      stencil: full/bin/3d

      bin: standard

WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)

Per MPI rank memory allocation (min/avg/max) = 22.18 | 22.18 | 22.18 Mbytes

Per MPI rank memory allocation (min/avg/max) = 69.68 | 69.81 | 69.93 Mbytes

PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42] 

   322.86952    1505558.1 4.2492771e+08     -4952473     28484035    322.86952    1505558.1 4.2492771e+08     -4952473     28484035 

Loop time of 2e-06 on 4 procs for 0 steps with 2 atoms

Loop time of 2.75e-06 on 4 procs for 0 steps with 2 atoms



100.0% CPU use with 4 MPI tasks x no OpenMP threads
@@ -182,19 +264,20 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 
Comm    | 0          | 0          | 0          |   0.0 |  0.00

Output  | 0          | 0          | 0          |   0.0 |  0.00

Modify  | 0          | 0          | 0          |   0.0 |  0.00

Other   |            | 2e-06      |            |       |100.00

Other   |            | 2.75e-06   |            |       |100.00



Nlocal:    0.5 ave 1 max 0 min

Nlocal:    0.5 ave 1.0 max 0.0 min

Histogram: 2 0 0 0 0 0 0 0 0 2

Nghost:    734.5 ave 735 max 734 min

Nghost:    734.5 ave 735.0 max 734.0 min

Histogram: 2 0 0 0 0 0 0 0 0 2

Neighs:    82.5 ave 177 max 0 min

Neighs:    82.5 ave 177.0 max 0.0 min

Histogram: 2 0 0 0 0 0 0 0 1 1

FullNghs:  165 ave 330 max 0 min

FullNghs:  165.0 ave 330.0 max 0.0 min

Histogram: 2 0 0 0 0 0 0 0 0 2



Total # of neighbors = 660

Ave neighs/atom = 330

Ave neighs/atom = 330.0

Neighbor list builds = 0

Dangerous builds = 0



Total wall time: 0:00:00

examples/mliap/log.03Jul20.mliap.snap.compute.g++.1

+110 −28
Original line number Diff line number Diff line 
LAMMPS (15 Jun 2020)

LAMMPS (30 Jun 2020)

# Demonstrate bispectrum computes



# initialize simulation
@@ -28,11 +28,11 @@ region box block 0 1 0 ${ny} 0 ${nz} 
region		box block 0 1 0 1 0 ${nz}

region		box block 0 1 0 1 0 1

create_box	2 box

Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)

Created orthogonal box = (0 0 0) to (2 2 2)

  1 by 1 by 1 MPI processor grid

create_atoms	2 box

Created 2 atoms

  create_atoms CPU = 0.001 seconds

  create_atoms CPU = 0.000 seconds



mass 		* 180.88
@@ -99,9 +99,19 @@ compute vbsum all reduce sum c_vb[*] 
# fix 		vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector

variable	db_2_25 equal c_db[2][25]



# set up compute snap generating global array

thermo 		100



# test output:   1: total potential energy

#                2: xy component of stress tensor

#                3: Sum(B_{000}^i, all i of type 2)

#                4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)

#                5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)

#

#                followed by 5 counterparts from compute snap



compute   	snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6

# run compute mliap with gradgradflag = 1



compute   	snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1

SNAP keyword rcutfac 1.0 

SNAP keyword twojmax 2 

SNAP keyword nelems 2
@@ -112,25 +122,97 @@ SNAP keyword rfac0 0.99363 
SNAP keyword rmin0 0 

SNAP keyword bzeroflag 0 

SNAP keyword switchflag 0 

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector



thermo 		100



# test output:   1: total potential energy

#                2: xy component of stress tensor

#                3: Sum(B_{000}^i, all i of type 2)

#                4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)

#                5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)

#

#                followed by 5 counterparts from compute snap

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector



thermo_style	custom 		pe            pxy            c_bsum2[1]   c_vbsum[55]    v_db_2_25 		c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]

thermo_modify 	norm no



# dump 		mydump_db all custom 1000 dump_db id c_db[*]

# dump_modify 	mydump_db sort id

run             ${nsteps}

run             0

Neighbor list info ...

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 6.8

  ghost atom cutoff = 6.8

  binsize = 3.4, bins = 1 1 1

  5 neighbor lists, perpetual/occasional/extra = 1 4 0

  (1) pair zbl, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/3d/newton

      bin: standard

  (2) compute sna/atom, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

  (3) compute snav/atom, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

  (4) compute snad/atom, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

  (5) compute mliap, occasional

      attributes: full, newton on

      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 10.73 | 10.73 | 10.73 Mbytes

PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12] 

   322.86952    1505558.1    364182.88   -240.25066    1381.7961    322.86952    1505558.1    364182.88   -240.25066    1381.7961 

Loop time of 2e-06 on 1 procs for 0 steps with 2 atoms



150.0% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0          | 0          | 0          |   0.0 |  0.00

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 0          | 0          | 0          |   0.0 |  0.00

Output  | 0          | 0          | 0          |   0.0 |  0.00

Modify  | 0          | 0          | 0          |   0.0 |  0.00

Other   |            | 2e-06      |            |       |100.00



Nlocal:    2.0 ave 2.0 max 2.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    853.0 ave 853.0 max 853.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    330.0 ave 330.0 max 330.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

FullNghs:  660.0 ave 660.0 max 660.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 660

Ave neighs/atom = 330.0

Neighbor list builds = 0

Dangerous builds = 0



uncompute	snap

unfix		snap



# Run MD

# run compute mliap with gradgradflag = 0



compute   	snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 0

SNAP keyword rcutfac 1.0 

SNAP keyword twojmax 2 

SNAP keyword nelems 2 

SNAP keyword elems A 

SNAP keyword radelems 2.3 

SNAP keyword welems 1.0 

SNAP keyword rfac0 0.99363 

SNAP keyword rmin0 0 

SNAP keyword bzeroflag 0 

SNAP keyword switchflag 0 

fix 		snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector



thermo_style	custom 		pe            pxy            c_bsum2[1]   c_vbsum[55]    v_db_2_25 		c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]

WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:694)

thermo_modify 	norm no



run             ${nsteps}

run             0
@@ -166,12 +248,12 @@ Neighbor list info ... 
      pair build: full/bin/atomonly

      stencil: full/bin/3d

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 10.73 | 10.73 | 10.73 Mbytes

Per MPI rank memory allocation (min/avg/max) = 22.85 | 22.85 | 22.85 Mbytes

PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12] 

   322.86952    1505558.1    364182.88   -240.25066    1381.7961    322.86952    1505558.1    364182.88   -240.25066    1381.7961 

Loop time of 0 on 1 procs for 0 steps with 2 atoms

Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms



0.0% CPU use with 1 MPI tasks x no OpenMP threads

100.0% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total
@@ -181,19 +263,19 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 
Comm    | 0          | 0          | 0          |   0.0 |  0.00

Output  | 0          | 0          | 0          |   0.0 |  0.00

Modify  | 0          | 0          | 0          |   0.0 |  0.00

Other   |            | 0          |            |       |  0.00

Other   |            | 1e-06      |            |       |100.00



Nlocal:    2 ave 2 max 2 min

Nlocal:    2.0 ave 2.0 max 2.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    853 ave 853 max 853 min

Nghost:    853.0 ave 853.0 max 853.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    330 ave 330 max 330 min

Neighs:    330.0 ave 330.0 max 330.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

FullNghs:  660 ave 660 max 660 min

FullNghs:  660.0 ave 660.0 max 660.0 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 660

Ave neighs/atom = 330

Ave neighs/atom = 330.0

Neighbor list builds = 0

Dangerous builds = 0

Total wall time: 0:00:00

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