Merge branch 'develop' into electrode
This commit is contained in:
Axel Kohlmeyer
@ -1,9 +1,7 @@
|
||||
# script for mgpt t=0 eos in bulk bcc structure
|
||||
|
||||
echo screen
|
||||
|
||||
units electron
|
||||
atom_style atomic
|
||||
units electron
|
||||
atom_style atomic
|
||||
|
||||
# Atomic volume for MGPT potential in a.u.
|
||||
variable atomic_vol equal 121.6
|
||||
@ -12,10 +10,10 @@ variable atomic_vol equal 121.6
|
||||
variable lattice_constant equal (${atomic_vol}*2.0)^(1.0/3.0)
|
||||
|
||||
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
|
||||
lattice bcc ${lattice_constant}
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
lattice bcc ${lattice_constant}
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# Define potential for use in simulation
|
||||
pair_style mgpt
|
||||
@ -26,20 +24,20 @@ pair_style mgpt
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
|
||||
|
||||
# Create velocities at 0 K
|
||||
velocity all create 0.0 87287
|
||||
velocity all create 0.0 87287
|
||||
|
||||
# Set neighbor list parameters
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
# Set up microcanonical integrator
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
# Dump coordinates to file every 50 timesteps
|
||||
dump id all atom 50 dump.bcc0
|
||||
#dump id all atom 50 dump.bcc0
|
||||
|
||||
# Output thermodynamical data every 10 timesteps
|
||||
thermo 10
|
||||
thermo 10
|
||||
|
||||
# Set output quantities and output format
|
||||
thermo_style custom step vol temp pe etotal press
|
||||
@ -48,7 +46,7 @@ thermo_style custom step vol temp pe etotal press
|
||||
#thermo_modify format float %15.5e
|
||||
|
||||
# Run 0 timesteps
|
||||
run 0
|
||||
run 0
|
||||
|
||||
# Convert energy to rydbergs and pressure to gpa
|
||||
|
||||
|
||||
@ -1,10 +1,8 @@
|
||||
# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
|
||||
# input for unrelaxed vacancy formation energy at constant atomic volume
|
||||
|
||||
echo screen
|
||||
|
||||
units electron
|
||||
atom_style atomic
|
||||
units electron
|
||||
atom_style atomic
|
||||
|
||||
# Atomic volume for MGPT potential in a.u.
|
||||
variable atomic_vol equal 121.6
|
||||
@ -16,10 +14,10 @@ variable lat_vol equal ${atomic_vol}*249/250
|
||||
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
|
||||
|
||||
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
|
||||
lattice bcc ${lattice_constant}
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
lattice bcc ${lattice_constant}
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# Remove central atom from bcc lattice to create vacancy
|
||||
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
|
||||
@ -34,20 +32,20 @@ pair_style mgpt
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
|
||||
|
||||
# Create velocities at 0 K
|
||||
velocity all create 0.0 87287
|
||||
velocity all create 0.0 87287
|
||||
|
||||
# Set neighbor list parameters
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
# Set up microcanonical integrator
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
# Dump coordinates to file every 50 timesteps
|
||||
dump id all atom 50 dump.vac0-bcc
|
||||
# dump id all atom 50 dump.vac0-bcc
|
||||
|
||||
# Output thermodynamical data every 10 timesteps
|
||||
thermo 10
|
||||
thermo 10
|
||||
|
||||
# Set output quantities and output format
|
||||
thermo_style custom step vol temp pe etotal press
|
||||
@ -56,7 +54,7 @@ thermo_style custom step vol temp pe etotal press
|
||||
#thermo_modify format float %15.5e
|
||||
|
||||
# Run 0 timesteps
|
||||
run 0
|
||||
run 0
|
||||
|
||||
# Convert energy to rydbergs and pressure to gpa
|
||||
|
||||
|
||||
@ -1,10 +1,8 @@
|
||||
# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
|
||||
# input for relaxed vacancy formation energy at constant pressure
|
||||
|
||||
echo screen
|
||||
|
||||
units electron
|
||||
atom_style atomic
|
||||
units electron
|
||||
atom_style atomic
|
||||
|
||||
# Atomic volume for MGPT potential
|
||||
variable atomic_vol equal 121.863
|
||||
@ -16,10 +14,10 @@ variable lat_vol equal ${atomic_vol}*249/250
|
||||
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
|
||||
|
||||
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
|
||||
lattice bcc ${lattice_constant}
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
lattice bcc ${lattice_constant}
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# Remove central atom from bcc lattice to create vacancy
|
||||
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
|
||||
@ -34,14 +32,14 @@ pair_style mgpt
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
|
||||
|
||||
# Set neighbor list parameters
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
# Dump coordinates to file every 50 timesteps
|
||||
dump id all atom 50 dump.vacmin-bcc
|
||||
# dump id all atom 50 dump.vacmin-bcc
|
||||
|
||||
# Output thermodynamical data every 10 timesteps
|
||||
thermo 10
|
||||
thermo 10
|
||||
|
||||
# Set output quantities and output format
|
||||
thermo_style custom step vol temp pe etotal press
|
||||
|
||||
134
examples/PACKAGES/mgpt/log.7Feb24.bcc0.g++.1
Normal file
134
examples/PACKAGES/mgpt/log.7Feb24.bcc0.g++.1
Normal file
@ -0,0 +1,134 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# script for mgpt t=0 eos in bulk bcc structure
|
||||
|
||||
units electron
|
||||
atom_style atomic
|
||||
|
||||
# Atomic volume for MGPT potential in a.u.
|
||||
variable atomic_vol equal 121.6
|
||||
|
||||
# Derive lattice constant from volume
|
||||
variable lattice_constant equal (${atomic_vol}*2.0)^(1.0/3.0)
|
||||
variable lattice_constant equal (121.6*2.0)^(1.0/3.0)
|
||||
|
||||
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
|
||||
lattice bcc ${lattice_constant}
|
||||
lattice bcc 6.24196300283154
|
||||
Lattice spacing in x,y,z = 6.241963 6.241963 6.241963
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (31.209815 31.209815 31.209815)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 250 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (31.209815 31.209815 31.209815)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
# Define potential for use in simulation
|
||||
pair_style mgpt
|
||||
|
||||
# Set parameters for potential:
|
||||
# parameter files atomic volume
|
||||
#pair_coeff * * parmin potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.6
|
||||
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
|
||||
|
||||
# Create velocities at 0 K
|
||||
velocity all create 0.0 87287
|
||||
|
||||
# Set neighbor list parameters
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
# Set up microcanonical integrator
|
||||
fix 1 all nve
|
||||
|
||||
# Dump coordinates to file every 50 timesteps
|
||||
#dump id all atom 50 dump.bcc0
|
||||
|
||||
# Output thermodynamical data every 10 timesteps
|
||||
thermo 10
|
||||
|
||||
# Set output quantities and output format
|
||||
thermo_style custom step vol temp pe etotal press
|
||||
|
||||
## Example: Output floating point number with 5 digits exponential notation.
|
||||
#thermo_modify format float %15.5e
|
||||
|
||||
# Run 0 timesteps
|
||||
run 0
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.161827
|
||||
ghost atom cutoff = 13.161827
|
||||
binsize = 6.5809134, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair mgpt, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair mgpt, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes
|
||||
Step Volume Temp PotEng TotEng Press
|
||||
0 30400 0 -74.412503 -74.412503 -1.1594626e+09
|
||||
Loop time of 1.019e-06 on 1 procs for 0 steps with 250 atoms
|
||||
|
||||
98.1% CPU use with 1 MPI tasks x 1 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 | | 1.019e-06 | | |100.00
|
||||
|
||||
Nlocal: 250 ave 250 max 250 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1479 ave 1479 max 1479 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8000 ave 8000 max 8000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 16000 ave 16000 max 16000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 16000
|
||||
Ave neighs/atom = 64
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Convert energy to rydbergs and pressure to gpa
|
||||
|
||||
variable natoms equal "count(all)"
|
||||
variable voltot equal "vol"
|
||||
variable atvol equal "v_voltot/v_natoms"
|
||||
variable etot equal "2.0*pe"
|
||||
variable etotry equal "v_etot/v_natoms"
|
||||
variable ptot equal "press"
|
||||
variable ptotgpa equal "v_ptot/1.0e+09"
|
||||
|
||||
print "number of atoms = ${natoms}"
|
||||
number of atoms = 250
|
||||
print "atomic volume (a.u.) = ${atvol}"
|
||||
atomic volume (a.u.) = 121.6
|
||||
print "total energy (ry/atom) = ${etotry}"
|
||||
total energy (ry/atom) = -0.59530002488734
|
||||
print "pressure (gpa) = ${ptotgpa}"
|
||||
pressure (gpa) = -1.15946260887554
|
||||
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
|
||||
250 121.6 -148.825006221835 -1.15946260887554
|
||||
print "${atvol} ${etotry} ${ptotgpa}"
|
||||
121.6 -0.59530002488734 -1.15946260887554
|
||||
Total wall time: 0:00:00
|
||||
134
examples/PACKAGES/mgpt/log.7Feb24.bcc0.g++.4
Normal file
134
examples/PACKAGES/mgpt/log.7Feb24.bcc0.g++.4
Normal file
@ -0,0 +1,134 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# script for mgpt t=0 eos in bulk bcc structure
|
||||
|
||||
units electron
|
||||
atom_style atomic
|
||||
|
||||
# Atomic volume for MGPT potential in a.u.
|
||||
variable atomic_vol equal 121.6
|
||||
|
||||
# Derive lattice constant from volume
|
||||
variable lattice_constant equal (${atomic_vol}*2.0)^(1.0/3.0)
|
||||
variable lattice_constant equal (121.6*2.0)^(1.0/3.0)
|
||||
|
||||
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
|
||||
lattice bcc ${lattice_constant}
|
||||
lattice bcc 6.24196300283154
|
||||
Lattice spacing in x,y,z = 6.241963 6.241963 6.241963
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (31.209815 31.209815 31.209815)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 250 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (31.209815 31.209815 31.209815)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
# Define potential for use in simulation
|
||||
pair_style mgpt
|
||||
|
||||
# Set parameters for potential:
|
||||
# parameter files atomic volume
|
||||
#pair_coeff * * parmin potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.6
|
||||
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
|
||||
|
||||
# Create velocities at 0 K
|
||||
velocity all create 0.0 87287
|
||||
|
||||
# Set neighbor list parameters
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
# Set up microcanonical integrator
|
||||
fix 1 all nve
|
||||
|
||||
# Dump coordinates to file every 50 timesteps
|
||||
#dump id all atom 50 dump.bcc0
|
||||
|
||||
# Output thermodynamical data every 10 timesteps
|
||||
thermo 10
|
||||
|
||||
# Set output quantities and output format
|
||||
thermo_style custom step vol temp pe etotal press
|
||||
|
||||
## Example: Output floating point number with 5 digits exponential notation.
|
||||
#thermo_modify format float %15.5e
|
||||
|
||||
# Run 0 timesteps
|
||||
run 0
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.161827
|
||||
ghost atom cutoff = 13.161827
|
||||
binsize = 6.5809134, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair mgpt, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair mgpt, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.73 | 3.73 | 3.73 Mbytes
|
||||
Step Volume Temp PotEng TotEng Press
|
||||
0 30400 0 -74.412503 -74.412503 -1.1594626e+09
|
||||
Loop time of 3.56525e-06 on 4 procs for 0 steps with 250 atoms
|
||||
|
||||
119.2% CPU use with 4 MPI tasks x 1 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 | | 3.565e-06 | | |100.00
|
||||
|
||||
Nlocal: 62.5 ave 65 max 60 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 868.5 ave 871 max 866 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 2000 ave 2110 max 1890 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 4000 ave 4160 max 3840 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 16000
|
||||
Ave neighs/atom = 64
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Convert energy to rydbergs and pressure to gpa
|
||||
|
||||
variable natoms equal "count(all)"
|
||||
variable voltot equal "vol"
|
||||
variable atvol equal "v_voltot/v_natoms"
|
||||
variable etot equal "2.0*pe"
|
||||
variable etotry equal "v_etot/v_natoms"
|
||||
variable ptot equal "press"
|
||||
variable ptotgpa equal "v_ptot/1.0e+09"
|
||||
|
||||
print "number of atoms = ${natoms}"
|
||||
number of atoms = 250
|
||||
print "atomic volume (a.u.) = ${atvol}"
|
||||
atomic volume (a.u.) = 121.6
|
||||
print "total energy (ry/atom) = ${etotry}"
|
||||
total energy (ry/atom) = -0.595300024887348
|
||||
print "pressure (gpa) = ${ptotgpa}"
|
||||
pressure (gpa) = -1.15946260887575
|
||||
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
|
||||
250 121.6 -148.825006221837 -1.15946260887575
|
||||
print "${atvol} ${etotry} ${ptotgpa}"
|
||||
121.6 -0.595300024887348 -1.15946260887575
|
||||
Total wall time: 0:00:00
|
||||
144
examples/PACKAGES/mgpt/log.7Feb24.vac0-bcc.g++.1
Normal file
144
examples/PACKAGES/mgpt/log.7Feb24.vac0-bcc.g++.1
Normal file
@ -0,0 +1,144 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
|
||||
# input for unrelaxed vacancy formation energy at constant atomic volume
|
||||
|
||||
units electron
|
||||
atom_style atomic
|
||||
|
||||
# Atomic volume for MGPT potential in a.u.
|
||||
variable atomic_vol equal 121.6
|
||||
|
||||
# Derive effective lattice volume from atomic volume for 249-site cell
|
||||
variable lat_vol equal ${atomic_vol}*249/250
|
||||
variable lat_vol equal 121.6*249/250
|
||||
|
||||
# Derive lattice constant from lattice volume
|
||||
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
|
||||
variable lattice_constant equal (121.1136*2.0)^(1.0/3.0)
|
||||
|
||||
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
|
||||
lattice bcc ${lattice_constant}
|
||||
lattice bcc 6.23362926394575
|
||||
Lattice spacing in x,y,z = 6.2336293 6.2336293 6.2336293
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 250 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
# Remove central atom from bcc lattice to create vacancy
|
||||
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
|
||||
delete_atoms region vacancy
|
||||
Deleted 1 atoms, new total = 249
|
||||
|
||||
# Define potential for use in simulation
|
||||
pair_style mgpt
|
||||
|
||||
# Set parameters for potential:
|
||||
# parameter files atomic volume
|
||||
#pair_coeff * * parmin potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.6
|
||||
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
|
||||
|
||||
# Create velocities at 0 K
|
||||
velocity all create 0.0 87287
|
||||
|
||||
# Set neighbor list parameters
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
# Set up microcanonical integrator
|
||||
fix 1 all nve
|
||||
|
||||
# Dump coordinates to file every 50 timesteps
|
||||
# dump id all atom 50 dump.vac0-bcc
|
||||
|
||||
# Output thermodynamical data every 10 timesteps
|
||||
thermo 10
|
||||
|
||||
# Set output quantities and output format
|
||||
thermo_style custom step vol temp pe etotal press
|
||||
|
||||
## Example: Output floating point number with 5 digits exponential notation.
|
||||
#thermo_modify format float %15.5e
|
||||
|
||||
# Run 0 timesteps
|
||||
run 0
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.161827
|
||||
ghost atom cutoff = 13.161827
|
||||
binsize = 6.5809134, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair mgpt, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair mgpt, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes
|
||||
Step Volume Temp PotEng TotEng Press
|
||||
0 30278.4 0 -73.996387 -73.996387 -6.3426731e+08
|
||||
Loop time of 1.016e-06 on 1 procs for 0 steps with 249 atoms
|
||||
|
||||
98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 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 | | 1.016e-06 | | |100.00
|
||||
|
||||
Nlocal: 249 ave 249 max 249 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1479 ave 1479 max 1479 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7936 ave 7936 max 7936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 15872 ave 15872 max 15872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 15872
|
||||
Ave neighs/atom = 63.742972
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Convert energy to rydbergs and pressure to gpa
|
||||
|
||||
variable natoms equal "count(all)"
|
||||
variable voltot equal "vol"
|
||||
variable atvol equal "v_voltot/v_natoms"
|
||||
variable etot equal "2.0*pe"
|
||||
variable etotry equal "v_etot/v_natoms"
|
||||
variable ptot equal "press"
|
||||
variable ptotgpa equal "v_ptot/1.0e+09"
|
||||
|
||||
print "number of atoms = ${natoms}"
|
||||
number of atoms = 249
|
||||
print "atomic volume (a.u.) = ${atvol}"
|
||||
atomic volume (a.u.) = 121.6
|
||||
print "total energy (ry/atom) = ${etotry}"
|
||||
total energy (ry/atom) = -0.594348488796036
|
||||
print "pressure (gpa) = ${ptotgpa}"
|
||||
pressure (gpa) = -0.634267307139553
|
||||
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
|
||||
249 121.6 -147.992773710213 -0.634267307139553
|
||||
print "${atvol} ${etotry} ${ptotgpa}"
|
||||
121.6 -0.594348488796036 -0.634267307139553
|
||||
Total wall time: 0:00:00
|
||||
144
examples/PACKAGES/mgpt/log.7Feb24.vac0-bcc.g++.4
Normal file
144
examples/PACKAGES/mgpt/log.7Feb24.vac0-bcc.g++.4
Normal file
@ -0,0 +1,144 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
|
||||
# input for unrelaxed vacancy formation energy at constant atomic volume
|
||||
|
||||
units electron
|
||||
atom_style atomic
|
||||
|
||||
# Atomic volume for MGPT potential in a.u.
|
||||
variable atomic_vol equal 121.6
|
||||
|
||||
# Derive effective lattice volume from atomic volume for 249-site cell
|
||||
variable lat_vol equal ${atomic_vol}*249/250
|
||||
variable lat_vol equal 121.6*249/250
|
||||
|
||||
# Derive lattice constant from lattice volume
|
||||
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
|
||||
variable lattice_constant equal (121.1136*2.0)^(1.0/3.0)
|
||||
|
||||
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
|
||||
lattice bcc ${lattice_constant}
|
||||
lattice bcc 6.23362926394575
|
||||
Lattice spacing in x,y,z = 6.2336293 6.2336293 6.2336293
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 250 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (31.168146 31.168146 31.168146)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
# Remove central atom from bcc lattice to create vacancy
|
||||
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
|
||||
delete_atoms region vacancy
|
||||
Deleted 1 atoms, new total = 249
|
||||
|
||||
# Define potential for use in simulation
|
||||
pair_style mgpt
|
||||
|
||||
# Set parameters for potential:
|
||||
# parameter files atomic volume
|
||||
#pair_coeff * * parmin potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.6
|
||||
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
|
||||
|
||||
# Create velocities at 0 K
|
||||
velocity all create 0.0 87287
|
||||
|
||||
# Set neighbor list parameters
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
# Set up microcanonical integrator
|
||||
fix 1 all nve
|
||||
|
||||
# Dump coordinates to file every 50 timesteps
|
||||
# dump id all atom 50 dump.vac0-bcc
|
||||
|
||||
# Output thermodynamical data every 10 timesteps
|
||||
thermo 10
|
||||
|
||||
# Set output quantities and output format
|
||||
thermo_style custom step vol temp pe etotal press
|
||||
|
||||
## Example: Output floating point number with 5 digits exponential notation.
|
||||
#thermo_modify format float %15.5e
|
||||
|
||||
# Run 0 timesteps
|
||||
run 0
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.161827
|
||||
ghost atom cutoff = 13.161827
|
||||
binsize = 6.5809134, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair mgpt, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair mgpt, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.73 | 3.73 | 3.73 Mbytes
|
||||
Step Volume Temp PotEng TotEng Press
|
||||
0 30278.4 0 -73.996387 -73.996387 -6.3426731e+08
|
||||
Loop time of 2.64725e-06 on 4 procs for 0 steps with 249 atoms
|
||||
|
||||
37.8% CPU use with 4 MPI tasks x 1 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 | | 2.647e-06 | | |100.00
|
||||
|
||||
Nlocal: 62.25 ave 65 max 60 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 867.75 ave 870 max 865 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 1984 ave 2099 max 1875 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
FullNghs: 3968 ave 4149 max 3825 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 15872
|
||||
Ave neighs/atom = 63.742972
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Convert energy to rydbergs and pressure to gpa
|
||||
|
||||
variable natoms equal "count(all)"
|
||||
variable voltot equal "vol"
|
||||
variable atvol equal "v_voltot/v_natoms"
|
||||
variable etot equal "2.0*pe"
|
||||
variable etotry equal "v_etot/v_natoms"
|
||||
variable ptot equal "press"
|
||||
variable ptotgpa equal "v_ptot/1.0e+09"
|
||||
|
||||
print "number of atoms = ${natoms}"
|
||||
number of atoms = 249
|
||||
print "atomic volume (a.u.) = ${atvol}"
|
||||
atomic volume (a.u.) = 121.6
|
||||
print "total energy (ry/atom) = ${etotry}"
|
||||
total energy (ry/atom) = -0.594348488795831
|
||||
print "pressure (gpa) = ${ptotgpa}"
|
||||
pressure (gpa) = -0.634267307088164
|
||||
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
|
||||
249 121.6 -147.992773710162 -0.634267307088164
|
||||
print "${atvol} ${etotry} ${ptotgpa}"
|
||||
121.6 -0.594348488795831 -0.634267307088164
|
||||
Total wall time: 0:00:00
|
||||
162
examples/PACKAGES/mgpt/log.7Feb24.vacmin-bcc.g++.1
Normal file
162
examples/PACKAGES/mgpt/log.7Feb24.vacmin-bcc.g++.1
Normal file
@ -0,0 +1,162 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
|
||||
# input for relaxed vacancy formation energy at constant pressure
|
||||
|
||||
units electron
|
||||
atom_style atomic
|
||||
|
||||
# Atomic volume for MGPT potential
|
||||
variable atomic_vol equal 121.863
|
||||
|
||||
# Derive effective lattice volume from atomic volume for 249-site cell
|
||||
variable lat_vol equal ${atomic_vol}*249/250
|
||||
variable lat_vol equal 121.863*249/250
|
||||
|
||||
# Derive lattice constant from lattice volume
|
||||
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
|
||||
variable lattice_constant equal (121.375548*2.0)^(1.0/3.0)
|
||||
|
||||
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
|
||||
lattice bcc ${lattice_constant}
|
||||
lattice bcc 6.23812011912273
|
||||
Lattice spacing in x,y,z = 6.2381201 6.2381201 6.2381201
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 250 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
# Remove central atom from bcc lattice to create vacancy
|
||||
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
|
||||
delete_atoms region vacancy
|
||||
Deleted 1 atoms, new total = 249
|
||||
|
||||
# Define potential for use in simulation
|
||||
pair_style mgpt
|
||||
|
||||
# Set parameters for potential:
|
||||
# parameter files atomic volume
|
||||
#pair_coeff * * parmin potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.863
|
||||
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
|
||||
|
||||
# Set neighbor list parameters
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
# Dump coordinates to file every 50 timesteps
|
||||
# dump id all atom 50 dump.vacmin-bcc
|
||||
|
||||
# Output thermodynamical data every 10 timesteps
|
||||
thermo 10
|
||||
|
||||
# Set output quantities and output format
|
||||
thermo_style custom step vol temp pe etotal press
|
||||
|
||||
## Example: Output floating point number with 5 digits exponential notation.
|
||||
#thermo_modify format float %15.5e
|
||||
|
||||
# minimize total energy
|
||||
min_style cg
|
||||
minimize 1.0e-10 1.0e-10 5000 10000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.171237
|
||||
ghost atom cutoff = 13.171237
|
||||
binsize = 6.5856184, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair mgpt, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair mgpt, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.88 | 4.88 | 4.88 Mbytes
|
||||
Step Volume Temp PotEng TotEng Press
|
||||
0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
|
||||
10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
|
||||
20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
|
||||
30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
|
||||
40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
|
||||
50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
|
||||
60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
|
||||
70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
|
||||
80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
|
||||
90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
|
||||
100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
|
||||
110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
|
||||
120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
|
||||
130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
|
||||
139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
|
||||
Loop time of 2.58636 on 1 procs for 139 steps with 249 atoms
|
||||
|
||||
90.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-73.9945109564338 -74.0063705487283 -74.0063705557007
|
||||
Force two-norm initial, final = 0.036622686 8.090814e-05
|
||||
Force max component initial, final = 0.0073094815 8.0524205e-06
|
||||
Final line search alpha, max atom move = 1 8.0524205e-06
|
||||
Iterations, force evaluations = 139 139
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5671 | 2.5671 | 2.5671 | 0.0 | 99.26
|
||||
Neigh | 0.015241 | 0.015241 | 0.015241 | 0.0 | 0.59
|
||||
Comm | 0.001446 | 0.001446 | 0.001446 | 0.0 | 0.06
|
||||
Output | 0.00038428 | 0.00038428 | 0.00038428 | 0.0 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.002161 | | | 0.08
|
||||
|
||||
Nlocal: 249 ave 249 max 249 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1479 ave 1479 max 1479 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7936 ave 7936 max 7936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 15872 ave 15872 max 15872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 15872
|
||||
Ave neighs/atom = 63.742972
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Convert energy to rydbergs and pressure to gpa
|
||||
|
||||
variable natoms equal "count(all)"
|
||||
variable voltot equal "vol"
|
||||
variable atvol equal "v_voltot/v_natoms"
|
||||
variable etot equal "2.0*pe"
|
||||
variable etotry equal "v_etot/v_natoms"
|
||||
variable ptot equal "press"
|
||||
variable ptotgpa equal "v_ptot/1.0e+09"
|
||||
|
||||
print "number of atoms = ${natoms}"
|
||||
number of atoms = 249
|
||||
print "atomic volume (a.u.) = ${atvol}"
|
||||
atomic volume (a.u.) = 121.863
|
||||
print "total energy (ry/atom) = ${etotry}"
|
||||
total energy (ry/atom) = -0.594428679162253
|
||||
print "pressure (gpa) = ${ptotgpa}"
|
||||
pressure (gpa) = -1.15783109516516
|
||||
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
|
||||
249 121.863 -148.012741111401 -1.15783109516516
|
||||
print "${atvol} ${etotry} ${ptotgpa}"
|
||||
121.863 -0.594428679162253 -1.15783109516516
|
||||
Total wall time: 0:00:02
|
||||
162
examples/PACKAGES/mgpt/log.7Feb24.vacmin-bcc.g++.4
Normal file
162
examples/PACKAGES/mgpt/log.7Feb24.vacmin-bcc.g++.4
Normal file
@ -0,0 +1,162 @@
|
||||
LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-744-g031cef558e-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
|
||||
# input for relaxed vacancy formation energy at constant pressure
|
||||
|
||||
units electron
|
||||
atom_style atomic
|
||||
|
||||
# Atomic volume for MGPT potential
|
||||
variable atomic_vol equal 121.863
|
||||
|
||||
# Derive effective lattice volume from atomic volume for 249-site cell
|
||||
variable lat_vol equal ${atomic_vol}*249/250
|
||||
variable lat_vol equal 121.863*249/250
|
||||
|
||||
# Derive lattice constant from lattice volume
|
||||
variable lattice_constant equal (${lat_vol}*2.0)^(1.0/3.0)
|
||||
variable lattice_constant equal (121.375548*2.0)^(1.0/3.0)
|
||||
|
||||
# Create bcc lattice with 5x5x5 unit cells (250 atoms)
|
||||
lattice bcc ${lattice_constant}
|
||||
lattice bcc 6.23812011912273
|
||||
Lattice spacing in x,y,z = 6.2381201 6.2381201 6.2381201
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 250 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (31.190601 31.190601 31.190601)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
# Remove central atom from bcc lattice to create vacancy
|
||||
region vacancy sphere 2.5 2.5 2.5 0.1 units lattice
|
||||
delete_atoms region vacancy
|
||||
Deleted 1 atoms, new total = 249
|
||||
|
||||
# Define potential for use in simulation
|
||||
pair_style mgpt
|
||||
|
||||
# Set parameters for potential:
|
||||
# parameter files atomic volume
|
||||
#pair_coeff * * parmin potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin ${atomic_vol}
|
||||
pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin 121.863
|
||||
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
|
||||
|
||||
# Set neighbor list parameters
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
# Dump coordinates to file every 50 timesteps
|
||||
# dump id all atom 50 dump.vacmin-bcc
|
||||
|
||||
# Output thermodynamical data every 10 timesteps
|
||||
thermo 10
|
||||
|
||||
# Set output quantities and output format
|
||||
thermo_style custom step vol temp pe etotal press
|
||||
|
||||
## Example: Output floating point number with 5 digits exponential notation.
|
||||
#thermo_modify format float %15.5e
|
||||
|
||||
# minimize total energy
|
||||
min_style cg
|
||||
minimize 1.0e-10 1.0e-10 5000 10000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13.171237
|
||||
ghost atom cutoff = 13.171237
|
||||
binsize = 6.5856184, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair mgpt, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
(2) pair mgpt, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.855 | 4.855 | 4.855 Mbytes
|
||||
Step Volume Temp PotEng TotEng Press
|
||||
0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
|
||||
10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
|
||||
20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
|
||||
30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
|
||||
40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
|
||||
50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
|
||||
60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
|
||||
70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
|
||||
80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
|
||||
90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
|
||||
100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
|
||||
110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
|
||||
120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
|
||||
130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
|
||||
139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
|
||||
Loop time of 0.972735 on 4 procs for 139 steps with 249 atoms
|
||||
|
||||
89.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-73.9945109564331 -74.0063705487423 -74.0063705556773
|
||||
Force two-norm initial, final = 0.036622686 8.090814e-05
|
||||
Force max component initial, final = 0.0073094815 8.0524207e-06
|
||||
Final line search alpha, max atom move = 1 8.0524207e-06
|
||||
Iterations, force evaluations = 139 139
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.9418 | 0.94514 | 0.9488 | 0.3 | 97.16
|
||||
Neigh | 0.0083827 | 0.0084423 | 0.0085002 | 0.0 | 0.87
|
||||
Comm | 0.011833 | 0.015482 | 0.01882 | 2.0 | 1.59
|
||||
Output | 0.0002579 | 0.00029089 | 0.000389 | 0.0 | 0.03
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.003376 | | | 0.35
|
||||
|
||||
Nlocal: 62.25 ave 68 max 59 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 867.75 ave 871 max 862 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 1984 ave 2211 max 1853 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
FullNghs: 3968 ave 4334 max 3761 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 15872
|
||||
Ave neighs/atom = 63.742972
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# Convert energy to rydbergs and pressure to gpa
|
||||
|
||||
variable natoms equal "count(all)"
|
||||
variable voltot equal "vol"
|
||||
variable atvol equal "v_voltot/v_natoms"
|
||||
variable etot equal "2.0*pe"
|
||||
variable etotry equal "v_etot/v_natoms"
|
||||
variable ptot equal "press"
|
||||
variable ptotgpa equal "v_ptot/1.0e+09"
|
||||
|
||||
print "number of atoms = ${natoms}"
|
||||
number of atoms = 249
|
||||
print "atomic volume (a.u.) = ${atvol}"
|
||||
atomic volume (a.u.) = 121.863
|
||||
print "total energy (ry/atom) = ${etotry}"
|
||||
total energy (ry/atom) = -0.594428679162068
|
||||
print "pressure (gpa) = ${ptotgpa}"
|
||||
pressure (gpa) = -1.15783109519336
|
||||
print "${natoms} ${atvol} ${etot} ${ptotgpa}"
|
||||
249 121.863 -148.012741111355 -1.15783109519336
|
||||
print "${atvol} ${etotry} ${ptotgpa}"
|
||||
121.863 -0.594428679162068 -1.15783109519336
|
||||
Total wall time: 0:00:00
|
||||
@ -1,53 +0,0 @@
|
||||
LAMMPS (23 Oct 2015)
|
||||
# script for mgpt t=0 eos in bulk bcc structure
|
||||
|
||||
echo screen
|
||||
Lattice spacing in x,y,z = 6.24196 6.24196 6.24196
|
||||
Created orthogonal box = (0 0 0) to (31.2098 31.2098 31.2098)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 250 atoms
|
||||
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
|
||||
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 = 13.1618
|
||||
ghost atom cutoff = 13.1618
|
||||
binsize = 6.58091 -> bins = 5 5 5
|
||||
Memory usage per processor = 3.54482 Mbytes
|
||||
Step Volume Temp PotEng TotEng Press
|
||||
0 30400 0 -74.412503 -74.412503 -1.1594626e+09
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 250 atoms
|
||||
|
||||
0.0% 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 | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 250 ave 250 max 250 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1479 ave 1479 max 1479 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8000 ave 8000 max 8000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 16000 ave 16000 max 16000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 16000
|
||||
Ave neighs/atom = 64
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
number of atoms = 250
|
||||
atomic volume (a.u.) = 121.6
|
||||
total energy (ry/atom) = -0.59530002488734
|
||||
pressure (gpa) = -1.15946260887556
|
||||
250 121.6 -148.825006221835 -1.15946260887556
|
||||
121.6 -0.59530002488734 -1.15946260887556
|
||||
Total wall time: 0:00:00
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (23 Oct 2015)
|
||||
# script for mgpt t=0 eos with unrelaxed vacancy in bcc lattice:
|
||||
# input for unrelaxed vacancy formation energy at constant atomic volume
|
||||
|
||||
echo screen
|
||||
Lattice spacing in x,y,z = 6.23363 6.23363 6.23363
|
||||
Created orthogonal box = (0 0 0) to (31.1681 31.1681 31.1681)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 250 atoms
|
||||
Deleted 1 atoms, new total = 249
|
||||
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
|
||||
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 = 13.1618
|
||||
ghost atom cutoff = 13.1618
|
||||
binsize = 6.58091 -> bins = 5 5 5
|
||||
Memory usage per processor = 3.54478 Mbytes
|
||||
Step Volume Temp PotEng TotEng Press
|
||||
0 30278.4 0 -73.996387 -73.996387 -6.3426731e+08
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 249 atoms
|
||||
|
||||
0.0% 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 | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 249 ave 249 max 249 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1479 ave 1479 max 1479 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7936 ave 7936 max 7936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 15872 ave 15872 max 15872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 15872
|
||||
Ave neighs/atom = 63.743
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
number of atoms = 249
|
||||
atomic volume (a.u.) = 121.6
|
||||
total energy (ry/atom) = -0.594348488796036
|
||||
pressure (gpa) = -0.634267307139601
|
||||
249 121.6 -147.992773710213 -0.634267307139601
|
||||
121.6 -0.594348488796036 -0.634267307139601
|
||||
Total wall time: 0:00:00
|
||||
@ -1,78 +0,0 @@
|
||||
LAMMPS (23 Oct 2015)
|
||||
# script for mgpt t=0 eos with relaxed vacancy in bcc structure:
|
||||
# input for relaxed vacancy formation energy at constant pressure
|
||||
|
||||
echo screen
|
||||
Lattice spacing in x,y,z = 6.23812 6.23812 6.23812
|
||||
Created orthogonal box = (0 0 0) to (31.1906 31.1906 31.1906)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 250 atoms
|
||||
Deleted 1 atoms, new total = 249
|
||||
Reading potential file Ta6.8x.mgpt.potin with DATE: 2015-07-30
|
||||
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 = 13.1712
|
||||
ghost atom cutoff = 13.1712
|
||||
binsize = 6.58562 -> bins = 5 5 5
|
||||
Memory usage per processor = 4.66978 Mbytes
|
||||
Step Volume Temp PotEng TotEng Press
|
||||
0 30343.887 0 -73.994511 -73.994511 -1.0504398e+09
|
||||
10 30343.887 0 -74.002332 -74.002332 -1.107516e+09
|
||||
20 30343.887 0 -74.00485 -74.00485 -1.1316373e+09
|
||||
30 30343.887 0 -74.005762 -74.005762 -1.143304e+09
|
||||
40 30343.887 0 -74.006116 -74.006116 -1.149395e+09
|
||||
50 30343.887 0 -74.006262 -74.006262 -1.1527914e+09
|
||||
60 30343.887 0 -74.006323 -74.006323 -1.1547677e+09
|
||||
70 30343.887 0 -74.00635 -74.00635 -1.1559529e+09
|
||||
80 30343.887 0 -74.006361 -74.006361 -1.1566763e+09
|
||||
90 30343.887 0 -74.006366 -74.006366 -1.1571256e+09
|
||||
100 30343.887 0 -74.006369 -74.006369 -1.1574093e+09
|
||||
110 30343.887 0 -74.00637 -74.00637 -1.1575908e+09
|
||||
120 30343.887 0 -74.00637 -74.00637 -1.1577083e+09
|
||||
130 30343.887 0 -74.00637 -74.00637 -1.1577849e+09
|
||||
139 30343.887 0 -74.006371 -74.006371 -1.1578311e+09
|
||||
Loop time of 4.22107 on 1 procs for 139 steps with 249 atoms
|
||||
|
||||
92.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-73.9945109564 -74.0063705487 -74.0063705557
|
||||
Force two-norm initial, final = 0.0366227 8.09081e-05
|
||||
Force max component initial, final = 0.00730948 8.05242e-06
|
||||
Final line search alpha, max atom move = 1 8.05242e-06
|
||||
Iterations, force evaluations = 139 139
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.1973 | 4.1973 | 4.1973 | 0.0 | 99.44
|
||||
Neigh | 0.018799 | 0.018799 | 0.018799 | 0.0 | 0.45
|
||||
Comm | 0.0017059 | 0.0017059 | 0.0017059 | 0.0 | 0.04
|
||||
Output | 0.00080252 | 0.00080252 | 0.00080252 | 0.0 | 0.02
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.002477 | | | 0.06
|
||||
|
||||
Nlocal: 249 ave 249 max 249 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1479 ave 1479 max 1479 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7936 ave 7936 max 7936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 15872 ave 15872 max 15872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 15872
|
||||
Ave neighs/atom = 63.743
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
number of atoms = 249
|
||||
atomic volume (a.u.) = 121.863
|
||||
total energy (ry/atom) = -0.594428679162064
|
||||
pressure (gpa) = -1.15783109519801
|
||||
249 121.863 -148.012741111354 -1.15783109519801
|
||||
121.863 -0.594428679162064 -1.15783109519801
|
||||
Total wall time: 0:00:04
|
||||
Reference in New Issue
Block a user