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Move A.Thomson's modifications on doc and examples in:

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- doc/src/.rst
- examples/USER/pace
- potentials
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Yury Lysogorskiy
2021-04-07 12:43:28 +02:00
parent 3de3302767
commit 0d1ccbe1b5
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examples/USER/pace/Cu-PBE-core-rep.ace Symbolic link
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../../../potentials/Cu-PBE-core-rep.ace

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examples/USER/pace/in.pace.product Normal file
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# simple test of fcc Cu with ACE product
units metal
atom_style atomic
neighbor 0.3 bin
neigh_modify every 2 delay 10 check yes
variable a equal 3.597
lattice fcc $a
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 26.98
group Al type 1
pair_style pace product
pair_coeff * * Cu-PBE-core-rep.ace Cu
velocity all create 300 8728 loop geom
timestep 0.0005
fix 1 all nve
compute eatom all pe/atom
compute energy all reduce sum c_eatom
variable delenergy equal c_energy-pe
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
thermo 10
thermo_style custom step temp epair etotal press v_delenergy v_delpress
run 100

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# simple test of fcc Cu with ACE recursive
units metal
atom_style atomic
neighbor 0.3 bin
neigh_modify every 2 delay 10 check yes
variable a equal 3.597
lattice fcc $a
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 26.98
group Al type 1
pair_style pace recursive
pair_coeff * * Cu-PBE-core-rep.ace Cu
velocity all create 300 8728 loop geom
timestep 0.0005
fix 1 all nve
compute eatom all pe/atom
compute energy all reduce sum c_eatom
variable delenergy equal c_energy-pe
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
thermo 10
thermo_style custom step temp epair etotal press v_delenergy v_delpress
run 100

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examples/USER/pace/log.03Feb2021.pace.product.g++.1 Normal file
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LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# simple test of fcc Cu with ACE product
units metal
atom_style atomic
neighbor 0.3 bin
neigh_modify every 2 delay 10 check yes
variable a equal 3.597
lattice fcc $a
lattice fcc 3.597
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
create_atoms CPU = 0.000 seconds
mass 1 26.98
group Al type 1
256 atoms in group Al
pair_style pace product
ACE version: 2021.2.3
Product evaluator is used
pair_coeff * * Cu-PBE-core-rep.ace Cu
Loading Cu-PBE-core-rep.ace
Total number of basis functions
Cu: 16 (r=1) 726 (r>1)
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
velocity all create 300 8728 loop geom
timestep 0.0005
fix 1 all nve
compute eatom all pe/atom
compute energy all reduce sum c_eatom
variable delenergy equal c_energy-pe
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
thermo 10
thermo_style custom step temp epair etotal press v_delenergy v_delpress
run 100
Neighbor list info ...
update every 2 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.7
ghost atom cutoff = 7.7
binsize = 3.85, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair pace, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
Step Temp E_pair TotEng Press v_delenergy v_delpress
0 300 -945.9873 -936.0989 45359.818 0 2.1827873e-11
10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11
20 228.73618 -943.63789 -936.09844 48903.598 0 -2.910383e-11
30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11
40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11
50 59.165961 -938.04759 -936.0974 56850.103 0 2.910383e-11
60 53.124678 -937.84857 -936.09751 56878.948 0 0
70 74.623347 -938.5575 -936.09782 55565.237 0 4.3655746e-11
80 109.4762 -939.70663 -936.09815 53665.652 0 2.910383e-11
90 142.02657 -940.77975 -936.09837 52001.1 0 0
100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11
Loop time of 11.4718 on 1 procs for 100 steps with 256 atoms
Performance: 0.377 ns/day, 63.732 hours/ns, 8.717 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.468 | 11.468 | 11.468 | 0.0 | 99.96
Neigh | 0.001181 | 0.001181 | 0.001181 | 0.0 | 0.01
Comm | 0.001207 | 0.001207 | 0.001207 | 0.0 | 0.01
Output | 0.000876 | 0.000876 | 0.000876 | 0.0 | 0.01
Modify | 0.000455 | 0.000455 | 0.000455 | 0.0 | 0.00
Other | | 0.000397 | | | 0.00
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2201.00 ave 2201 max 2201 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 43118.0 ave 43118 max 43118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43118
Ave neighs/atom = 168.42969
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:11

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LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# simple test of fcc Cu with ACE product
units metal
atom_style atomic
neighbor 0.3 bin
neigh_modify every 2 delay 10 check yes
variable a equal 3.597
lattice fcc $a
lattice fcc 3.597
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
create_atoms CPU = 0.000 seconds
mass 1 26.98
group Al type 1
256 atoms in group Al
pair_style pace product
ACE version: 2021.2.3
Product evaluator is used
pair_coeff * * Cu-PBE-core-rep.ace Cu
Loading Cu-PBE-core-rep.ace
Total number of basis functions
Cu: 16 (r=1) 726 (r>1)
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
velocity all create 300 8728 loop geom
timestep 0.0005
fix 1 all nve
compute eatom all pe/atom
compute energy all reduce sum c_eatom
variable delenergy equal c_energy-pe
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
thermo 10
thermo_style custom step temp epair etotal press v_delenergy v_delpress
run 100
Neighbor list info ...
update every 2 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.7
ghost atom cutoff = 7.7
binsize = 3.85, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair pace, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
Step Temp E_pair TotEng Press v_delenergy v_delpress
0 300 -945.9873 -936.0989 45359.818 0 -1.4551915e-11
10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11
20 228.73618 -943.63789 -936.09844 48903.598 0 0
30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11
40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11
50 59.165961 -938.04759 -936.0974 56850.103 0 -1.4551915e-11
60 53.124678 -937.84857 -936.09751 56878.948 0 7.2759576e-12
70 74.623347 -938.5575 -936.09782 55565.237 0 0
80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11
90 142.02657 -940.77975 -936.09837 52001.1 0 -1.4551915e-11
100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11
Loop time of 3.54317 on 4 procs for 100 steps with 256 atoms
Performance: 1.219 ns/day, 19.684 hours/ns, 28.223 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1375 | 3.3058 | 3.469 | 6.5 | 93.30
Neigh | 0.000284 | 0.00031975 | 0.000352 | 0.0 | 0.01
Comm | 0.071607 | 0.23492 | 0.40336 | 24.6 | 6.63
Output | 0.001189 | 0.0012315 | 0.001347 | 0.2 | 0.03
Modify | 0.000311 | 0.00032725 | 0.000351 | 0.0 | 0.01
Other | | 0.0005298 | | | 0.01
Nlocal: 64.0000 ave 71 max 57 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 1373.00 ave 1380 max 1366 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 10779.5 ave 11978 max 9604 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 43118
Ave neighs/atom = 168.42969
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# simple test of fcc Cu with ACE recursive
units metal
atom_style atomic
neighbor 0.3 bin
neigh_modify every 2 delay 10 check yes
variable a equal 3.597
lattice fcc $a
lattice fcc 3.597
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
create_atoms CPU = 0.000 seconds
mass 1 26.98
group Al type 1
256 atoms in group Al
pair_style pace recursive
ACE version: 2021.2.3
Recursive evaluator is used
pair_coeff * * Cu-PBE-core-rep.ace Cu
Loading Cu-PBE-core-rep.ace
Total number of basis functions
Cu: 16 (r=1) 726 (r>1)
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
velocity all create 300 8728 loop geom
timestep 0.0005
fix 1 all nve
compute eatom all pe/atom
compute energy all reduce sum c_eatom
variable delenergy equal c_energy-pe
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
thermo 10
thermo_style custom step temp epair etotal press v_delenergy v_delpress
run 100
Neighbor list info ...
update every 2 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.7
ghost atom cutoff = 7.7
binsize = 3.85, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair pace, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
Step Temp E_pair TotEng Press v_delenergy v_delpress
0 300 -945.9873 -936.0989 45359.818 0 0
10 280.68558 -945.35055 -936.09878 46326.919 0 5.8207661e-11
20 228.73618 -943.63789 -936.09844 48903.598 0 1.4551915e-11
30 160.53661 -941.38948 -936.09798 52222.083 0 7.2759576e-11
40 97.732944 -939.31899 -936.09758 55176.875 0 -5.8207661e-11
50 59.165961 -938.04759 -936.0974 56850.103 0 0
60 53.124678 -937.84857 -936.09751 56878.948 0 8.7311491e-11
70 74.623347 -938.5575 -936.09782 55565.237 0 -1.4551915e-11
80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11
90 142.02657 -940.77975 -936.09837 52001.1 0 2.910383e-11
100 161.73598 -941.42945 -936.09842 51114.997 0 0
Loop time of 9.31437 on 1 procs for 100 steps with 256 atoms
Performance: 0.464 ns/day, 51.746 hours/ns, 10.736 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.3103 | 9.3103 | 9.3103 | 0.0 | 99.96
Neigh | 0.001214 | 0.001214 | 0.001214 | 0.0 | 0.01
Comm | 0.001176 | 0.001176 | 0.001176 | 0.0 | 0.01
Output | 0.000827 | 0.000827 | 0.000827 | 0.0 | 0.01
Modify | 0.000479 | 0.000479 | 0.000479 | 0.0 | 0.01
Other | | 0.000363 | | | 0.00
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2201.00 ave 2201 max 2201 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 43118.0 ave 43118 max 43118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43118
Ave neighs/atom = 168.42969
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:09

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LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# simple test of fcc Cu with ACE recursive
units metal
atom_style atomic
neighbor 0.3 bin
neigh_modify every 2 delay 10 check yes
variable a equal 3.597
lattice fcc $a
lattice fcc 3.597
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
create_atoms CPU = 0.000 seconds
mass 1 26.98
group Al type 1
256 atoms in group Al
pair_style pace recursive
ACE version: 2021.2.3
Recursive evaluator is used
pair_coeff * * Cu-PBE-core-rep.ace Cu
Loading Cu-PBE-core-rep.ace
Total number of basis functions
Cu: 16 (r=1) 726 (r>1)
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
velocity all create 300 8728 loop geom
timestep 0.0005
fix 1 all nve
compute eatom all pe/atom
compute energy all reduce sum c_eatom
variable delenergy equal c_energy-pe
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
thermo 10
thermo_style custom step temp epair etotal press v_delenergy v_delpress
run 100
Neighbor list info ...
update every 2 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.7
ghost atom cutoff = 7.7
binsize = 3.85, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair pace, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
Step Temp E_pair TotEng Press v_delenergy v_delpress
0 300 -945.9873 -936.0989 45359.818 0 -5.0931703e-11
10 280.68558 -945.35055 -936.09878 46326.919 0 1.4551915e-11
20 228.73618 -943.63789 -936.09844 48903.598 0 0
30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11
40 97.732944 -939.31899 -936.09758 55176.875 0 0
50 59.165961 -938.04759 -936.0974 56850.103 0 -2.910383e-11
60 53.124678 -937.84857 -936.09751 56878.948 0 1.4551915e-11
70 74.623347 -938.5575 -936.09782 55565.237 0 3.6379788e-11
80 109.4762 -939.70663 -936.09815 53665.652 0 -7.2759576e-12
90 142.02657 -940.77975 -936.09837 52001.1 0 -2.910383e-11
100 161.73598 -941.42945 -936.09842 51114.997 0 7.2759576e-12
Loop time of 2.91339 on 4 procs for 100 steps with 256 atoms
Performance: 1.483 ns/day, 16.185 hours/ns, 34.324 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5753 | 2.723 | 2.8656 | 6.3 | 93.46
Neigh | 0.000308 | 0.000365 | 0.00046 | 0.0 | 0.01
Comm | 0.045106 | 0.18792 | 0.33552 | 24.1 | 6.45
Output | 0.001213 | 0.001259 | 0.001388 | 0.2 | 0.04
Modify | 0.000304 | 0.00033 | 0.00037 | 0.0 | 0.01
Other | | 0.0005595 | | | 0.02
Nlocal: 64.0000 ave 71 max 57 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 1373.00 ave 1380 max 1366 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 10779.5 ave 11978 max 9604 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 43118
Ave neighs/atom = 168.42969
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:03