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Fix input file bug and update examples

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exapde
2024-05-22 21:25:31 -04:00
parent c2e4ad220f
commit 86abf4f680
51 changed files with 4903 additions and 3797 deletions
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19
doc/src/compute_pod_atom.rst
View File

@ -20,16 +20,15 @@ Syntax
.. code-block:: LAMMPS
compute ID group-ID pod/atom param.pod projection_matrix.pod centroids.pod
compute ID group-ID podd/atom param.pod projection_matrix.pod centroids.pod
compute ID group-ID pod/ldd param.pod projection_matrix.pod centroids.pod
compute ID group-ID pod/gdd param.pod projection_matrix.pod centroids.pod
compute ID group-ID pod/atom param.pod coefficients.pod
compute ID group-ID podd/atom param.pod coefficients.pod
compute ID group-ID pod/ldd param.pod coefficients.pod
compute ID group-ID pod/gdd param.pod coefficients.pod
* ID, group-ID are documented in :doc:`compute <compute>` command
* pod/atom = style name of this compute command
* param.pod = the parameter file specifies parameters of the POD descriptors
* projection_matrix.pod = the projection matrix file
* centroids.pod = the centroid file
* coefficients.pod = the coefficient file specifies coefficients of the POD potential
Examples
""""""""
@ -40,10 +39,10 @@ Examples
compute dd all podd/atom Ta_param.pod
compute ldd all pod/ldd Ta_param.pod
compute gdd all podd/gdd Ta_param.pod
compute d all pod/atom Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod
compute dd all podd/atom Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod
compute ldd all pod/ldd Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod
compute gdd all podd/gdd Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod
compute d all pod/atom Ta_param.pod Ta_coefficients.pod
compute dd all podd/atom Ta_param.pod Ta_coefficients.pod
compute ldd all pod/ldd Ta_param.pod Ta_coefficients.pod
compute gdd all podd/gdd Ta_param.pod Ta_coefficients.pod
Description
"""""""""""

16
doc/src/fitpod_command.rst
View File

@ -8,14 +8,12 @@ Syntax
.. code-block:: LAMMPS
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
* fitpod = style name of this command
* Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs)
* Ta_data.pod = an input file that specifies DFT data used to fit a POD potential
* Ta_coefficients.pod (optional) = an input file that specifies trainable coefficients of a POD potential
* Ta_projection_matrix.pod (optional) = an input file that specifies a projection matrix for dimensionlity reduction via principal component analysis
* Ta_centroids.pod (optional) = an input file that specifies centroids of clusters computed using k-means algorithm
Examples
""""""""
@ -24,7 +22,6 @@ Examples
fitpod Ta_param.pod Ta_data.pod
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod
Description
"""""""""""
@ -220,13 +217,9 @@ successful training, a number of output files are produced, if enabled:
* ``<basename>_test_errors.pod`` reports errors for the test data set
* ``<basename>_test_analysis.pod`` reports detailed errors for all test configurations
* ``<basename>_coefficients.pod`` contains the coefficients of the POD potential
* ``<basename>_projection_matrix.pod`` contains the projection matrix from the principal component analysis
* ``<basename>_centroids.pod`` contains the centroids of the atom clusters
After training the POD potential, ``Ta_param.pod`` and ``<basename>_coefficients.pod``
are the two files needed to use the POD potential in LAMMPS.
If the number of environment clusters is greater than 1, then
``<basename>_projection_matrix.pod`` and ``<basename>_centroids.pod`` are also needed.
See :doc:`pair_style pod <pair_pod>` for using the POD potential. Examples
about training and using POD potentials are found in the directory
lammps/examples/PACKAGES/pod and the Github repo https://github.com/cesmix-mit/pod-examples.
@ -337,13 +330,6 @@ for example,
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
However, if the number of clusters is greater than 1, then both the projection matrix and the centroids
must also be provided
.. code-block:: LAMMPS
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod
Restrictions
""""""""""""

39
doc/src/pair_pod.rst
View File

@ -18,7 +18,7 @@ Examples
.. code-block:: LAMMPS
pair_style pod
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod Ta
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
Description
"""""""""""
@ -44,41 +44,20 @@ POD potential. The top of the coefficient file can contain any number of
blank and comment lines (start with #), but follows a strict format
after that. The first non-blank non-comment line must contain:
* POD_coefficients: *ncoeff*
* model_coefficients: *ncoeff* *nproj* *ncentroid*
This is followed by *ncoeff* coefficients, one per line. The coefficient
This is followed by *ncoeff* coefficients, *nproj* projection matrix entries,
and *ncentroid* centroid coordinates, one per line. The coefficient
file is generated after training the POD potential using :doc:`fitpod
<fitpod_command>`.
The projection matrix file (``Ta_projection_matrix.pod``) contains a matrix of the
principal component analysis. This matrix is used to project the per-atom descriptors
onto a low-dimensional descriptor space. The top of the projection matrix file can
contain any number of blank and comment lines (start with #), but follows a strict format
after that. The first non-blank non-comment line must contain:
* projection_matrix: *nentry*
This is followed by *nentry* entries, one per line. The projection matrix
file is generated by using :doc:`fitpod <fitpod_command>` when the number of environment clusters is greater than 1.
The centroid matrix file (``Ta_centroids.pod``) contains centroids of the atom clusters
computed by applying the k-means algorithm to the low-dimensional descriptor space.
The top of the centroid file can contain any number of blank and comment lines (start with #),
but follows a strict format after that. The first non-blank non-comment line must contain:
* centroids: *nentry*
This is followed by *nentry* entries, one per line. The centroid
file is generated by using :doc:`fitpod
<fitpod_command>` when the number of environment clusters is greater than 1.
As an example, if a LAMMPS indium phosphide simulation has 4 atoms
types, with the first two being indium and the third and fourth being
phophorous, the pair_coeff command would look like this:
.. code-block:: LAMMPS
pair_coeff * * pod InP_param.pod InP_coefficients.pod "" "" In In P P
pair_coeff * * pod InP_param.pod InP_coefficients.pod In In P P
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
The two filenames are for the parameter and coefficient files, respectively.
@ -86,14 +65,6 @@ The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
POD 'In' element. The two trailing 'P' arguments map LAMMPS atom types
3 and 4 to the POD 'P' element.
If the number of environment clusters is greater than 1, then both the projection matrix and the centroids
must also be provided
.. code-block:: LAMMPS
pair_coeff * * pod InP_param.pod InP_coefficients.pod InP_projection_matrix.pod InP_centroids.pod In In P P
If a POD mapping value is specified as NULL, the mapping is not
performed. This can be used when a *pod* potential is used as part of
the *hybrid* pair style. The NULL values are placeholders for atom

9
examples/PACKAGES/pod/InP/InP_centroids.pod
View File

@ -1,9 +0,0 @@
centroids: 8
-23.434570721059636
0.158270519167870
-41.863652345708438
-1.266628798618644
-13.129952230200592
1.306603727667970
-24.529602202015035
-0.220133155905198

610
examples/PACKAGES/pod/InP/InP_coefficients.pod
View File

@ -1,305 +1,305 @@
POD_coefficients: 304
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44.683348
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model_coefficients: 304 0 0
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605
examples/PACKAGES/pod/InP/InP_projection_matrix.pod
View File

@ -1,605 +0,0 @@
projection_matrix: 604
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3788
examples/PACKAGES/pod/InP/InP_training_analysis.pod
View File

File diff suppressed because it is too large Load Diff

8
examples/PACKAGES/pod/InP/InP_training_errors.pod
View File

@ -3,8 +3,8 @@
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
--------------------------------------------------------------------------------------------
Bulk.xyz 1 8 0.001678 0.001678 0.000000 0.000000
EOS.xyz 268 2080 0.001463 0.001817 0.001107 0.015464
Shear.xyz 346 2768 0.000415 0.000640 0.008335 0.012863
EOS.xyz 268 2080 0.001463 0.001817 0.001107 0.015463
Shear.xyz 346 2768 0.000415 0.000640 0.008336 0.012865
Strain.xyz 163 1304 0.001129 0.001374 0.000021 0.000036
aIn.xyz 54 11664 0.000737 0.000796 0.007969 0.016112
aP.xyz 21 4536 0.001396 0.001407 0.019599 0.054174
@ -17,11 +17,11 @@ s_aa.xyz 18 1152 0.001198 0.001200 0.037169
s_iIn.xyz 144 9360 0.002014 0.002255 0.035374 0.050726
s_iP.xyz 337 21905 0.001655 0.002178 0.025130 0.038368
s_vIn.xyz 17 1071 0.007984 0.007992 0.023190 0.039575
s_vP.xyz 77 4851 0.000245 0.000281 0.018303 0.025818
s_vP.xyz 77 4851 0.000245 0.000281 0.018303 0.025819
s_vv.xyz 65 4030 0.001759 0.001986 0.039037 0.052667
vP.xyz 10 2150 0.000640 0.000640 0.005452 0.009834
vv.xyz 19 4066 0.001336 0.001403 0.020930 0.034386
--------------------------------------------------------------------------------------------
All files 1894 118214 0.001288 0.001855 0.018109 0.032648
All files 1894 118214 0.001288 0.001855 0.018109 0.032649
--------------------------------------------------------------------------------------------
**************** End of Error Analysis for the Training Data Set ****************

4
examples/PACKAGES/pod/InP/README.md
View File

@ -6,11 +6,11 @@ Please download the training data from [the repo](https://github.com/cesmix-mit/
Fit POD with
lmp -in InP_fit.pod
lmp -in in.fitpod
This creates `InP_coefficients.pod` for the linear model, which we can use to run MD with
lmp -in InP_mdrun.pod
lmp -in in.pod

0
examples/PACKAGES/pod/InP/InP_fit.pod → examples/PACKAGES/pod/InP/in.fitpod
View File

2
examples/PACKAGES/pod/InP/InP_mdrun.pod → examples/PACKAGES/pod/InP/in.pod
View File

@ -25,7 +25,7 @@ mass 2 30.98
# POD potential
pair_style pod
pair_coeff * * InP_param.pod InP_coefficients.pod InP_projection_matrix.pod InP_centroids.pod In P
pair_coeff * * InP_param.pod InP_coefficients.pod In P
# Setup output

163
examples/PACKAGES/pod/InP/log.22May24.fitpod.g++.1 Normal file
View File

@ -0,0 +1,163 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
fitpod InP_param.pod InP_data.pod
**************** Begin of POD Potentials ****************
species: In P
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 0.8
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 2
five-body radial basis functions: 0
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 12
number of local descriptors per element for three-body potential: 75
number of local descriptors per element for four-body potential: 64
number of local descriptors per element for five-body potential: 0
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 152
number of global descriptors: 304
**************** End of POD Potentials ****************
**************** Begin of Data File ****************
file format: extxyz
file extension: xyz
path to training data set: XYZ
path to test data set: XYZ
path to environment configuration set: XYZ
basename for output files: InP
training fraction: 1
test fraction: 1
randomize training data set: 1
randomize test data set: 1
error analysis for training data set: 1
error analysis for test data set: 0
energy/force calculation for training data set: 0
energy/force calculation for test data set: 0
fitting weight for energy: 100
fitting weight for force: 1
fitting weight for stress: 0
save pod descriptors: 0
compute pod descriptors: 0
**************** End of Data File ****************
**************** Begin of Training Data Set ****************
--------------------------------------------------------
data file | number of configurations | number of atoms
--------------------------------------------------------
Bulk.xyz | 1 | 8
EOS.xyz | 268 | 2080
Shear.xyz | 346 | 2768
Strain.xyz | 163 | 1304
aIn.xyz | 54 | 11664
aP.xyz | 21 | 4536
aa.xyz | 20 | 4320
iIn.xyz | 41 | 8897
iP.xyz | 100 | 21700
s_aIn.xyz | 121 | 7744
s_aP.xyz | 72 | 4608
s_aa.xyz | 18 | 1152
s_iIn.xyz | 144 | 9360
s_iP.xyz | 337 | 21905
s_vIn.xyz | 17 | 1071
s_vP.xyz | 77 | 4851
s_vv.xyz | 65 | 4030
vP.xyz | 10 | 2150
vv.xyz | 19 | 4066
--------------------------------------------------------
number of files: 19
number of configurations in all files: 1894
number of atoms in all files: 118214
minimum number of atoms: 4
maximum number of atoms: 217
**************** End of Training Data Set ****************
**************** Begin of Memory Allocation ****************
maximum number of atoms in periodic domain: 217
maximum number of atoms in extended domain: 5859
maximum number of neighbors in extended domain: 1271403
size of double memory: 5555904
size of descriptor matrix: 304 x 304
**************** End of Memory Allocation ****************
**************** Begin of Least-Squares Fitting ****************
Configuration: # 1
Configuration: # 101
Configuration: # 201
Configuration: # 301
Configuration: # 401
Configuration: # 501
Configuration: # 601
Configuration: # 701
Configuration: # 801
Configuration: # 901
Configuration: # 1001
Configuration: # 1101
Configuration: # 1201
Configuration: # 1301
Configuration: # 1401
Configuration: # 1501
Configuration: # 1601
Configuration: # 1701
Configuration: # 1801
**************** Begin of Error Calculation ****************
Configuration: # 1
Configuration: # 101
Configuration: # 201
Configuration: # 301
Configuration: # 401
Configuration: # 501
Configuration: # 601
Configuration: # 701
Configuration: # 801
Configuration: # 901
Configuration: # 1001
Configuration: # 1101
Configuration: # 1201
Configuration: # 1301
Configuration: # 1401
Configuration: # 1501
Configuration: # 1601
Configuration: # 1701
Configuration: # 1801
**************** End of Error Calculation ****************
**************** Begin of Error Analysis for the Training Data Set ****************
--------------------------------------------------------------------------------------------
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
--------------------------------------------------------------------------------------------
Bulk.xyz 1 8 0.001678 0.001678 0.000000 0.000000
EOS.xyz 268 2080 0.001463 0.001817 0.001107 0.015464
Shear.xyz 346 2768 0.000415 0.000640 0.008335 0.012863
Strain.xyz 163 1304 0.001129 0.001374 0.000021 0.000036
aIn.xyz 54 11664 0.000737 0.000796 0.007969 0.016112
aP.xyz 21 4536 0.001396 0.001407 0.019599 0.054174
aa.xyz 20 4320 0.001991 0.001991 0.016735 0.027955
iIn.xyz 41 8897 0.001548 0.001687 0.013910 0.025462
iP.xyz 100 21700 0.001090 0.001203 0.009692 0.018549
s_aIn.xyz 121 7744 0.000856 0.000889 0.011041 0.017399
s_aP.xyz 72 4608 0.002255 0.003587 0.032425 0.045878
s_aa.xyz 18 1152 0.001198 0.001200 0.037169 0.047713
s_iIn.xyz 144 9360 0.002014 0.002255 0.035374 0.050726
s_iP.xyz 337 21905 0.001655 0.002178 0.025130 0.038368
s_vIn.xyz 17 1071 0.007984 0.007992 0.023190 0.039575
s_vP.xyz 77 4851 0.000245 0.000281 0.018303 0.025818
s_vv.xyz 65 4030 0.001759 0.001986 0.039037 0.052667
vP.xyz 10 2150 0.000640 0.000640 0.005452 0.009834
vv.xyz 19 4066 0.001336 0.001403 0.020930 0.034386
--------------------------------------------------------------------------------------------
All files 1894 118214 0.001288 0.001855 0.018109 0.032648
--------------------------------------------------------------------------------------------
**************** End of Error Analysis for the Training Data Set ****************
Total wall time: 0:00:27

163
examples/PACKAGES/pod/InP/log.22May24.fitpod.g++.4 Normal file
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@ -0,0 +1,163 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
fitpod InP_param.pod InP_data.pod
**************** Begin of POD Potentials ****************
species: In P
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 0.8
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 2
five-body radial basis functions: 0
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 12
number of local descriptors per element for three-body potential: 75
number of local descriptors per element for four-body potential: 64
number of local descriptors per element for five-body potential: 0
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 152
number of global descriptors: 304
**************** End of POD Potentials ****************
**************** Begin of Data File ****************
file format: extxyz
file extension: xyz
path to training data set: XYZ
path to test data set: XYZ
path to environment configuration set: XYZ
basename for output files: InP
training fraction: 1
test fraction: 1
randomize training data set: 1
randomize test data set: 1
error analysis for training data set: 1
error analysis for test data set: 0
energy/force calculation for training data set: 0
energy/force calculation for test data set: 0
fitting weight for energy: 100
fitting weight for force: 1
fitting weight for stress: 0
save pod descriptors: 0
compute pod descriptors: 0
**************** End of Data File ****************
**************** Begin of Training Data Set ****************
--------------------------------------------------------
data file | number of configurations | number of atoms
--------------------------------------------------------
Bulk.xyz | 1 | 8
EOS.xyz | 268 | 2080
Shear.xyz | 346 | 2768
Strain.xyz | 163 | 1304
aIn.xyz | 54 | 11664
aP.xyz | 21 | 4536
aa.xyz | 20 | 4320
iIn.xyz | 41 | 8897
iP.xyz | 100 | 21700
s_aIn.xyz | 121 | 7744
s_aP.xyz | 72 | 4608
s_aa.xyz | 18 | 1152
s_iIn.xyz | 144 | 9360
s_iP.xyz | 337 | 21905
s_vIn.xyz | 17 | 1071
s_vP.xyz | 77 | 4851
s_vv.xyz | 65 | 4030
vP.xyz | 10 | 2150
vv.xyz | 19 | 4066
--------------------------------------------------------
number of files: 19
number of configurations in all files: 1894
number of atoms in all files: 118214
minimum number of atoms: 4
maximum number of atoms: 217
**************** End of Training Data Set ****************
**************** Begin of Memory Allocation ****************
maximum number of atoms in periodic domain: 217
maximum number of atoms in extended domain: 5859
maximum number of neighbors in extended domain: 1271403
size of double memory: 5555904
size of descriptor matrix: 304 x 304
**************** End of Memory Allocation ****************
**************** Begin of Least-Squares Fitting ****************
Configuration: # 1
Configuration: # 101
Configuration: # 201
Configuration: # 301
Configuration: # 401
Configuration: # 501
Configuration: # 601
Configuration: # 701
Configuration: # 801
Configuration: # 901
Configuration: # 1001
Configuration: # 1101
Configuration: # 1201
Configuration: # 1301
Configuration: # 1401
Configuration: # 1501
Configuration: # 1601
Configuration: # 1701
Configuration: # 1801
**************** Begin of Error Calculation ****************
Configuration: # 1
Configuration: # 101
Configuration: # 201
Configuration: # 301
Configuration: # 401
Configuration: # 501
Configuration: # 601
Configuration: # 701
Configuration: # 801
Configuration: # 901
Configuration: # 1001
Configuration: # 1101
Configuration: # 1201
Configuration: # 1301
Configuration: # 1401
Configuration: # 1501
Configuration: # 1601
Configuration: # 1701
Configuration: # 1801
**************** End of Error Calculation ****************
**************** Begin of Error Analysis for the Training Data Set ****************
--------------------------------------------------------------------------------------------
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
--------------------------------------------------------------------------------------------
Bulk.xyz 1 8 0.001678 0.001678 0.000000 0.000000
EOS.xyz 268 2080 0.001463 0.001817 0.001107 0.015463
Shear.xyz 346 2768 0.000415 0.000640 0.008336 0.012865
Strain.xyz 163 1304 0.001129 0.001374 0.000021 0.000036
aIn.xyz 54 11664 0.000737 0.000796 0.007969 0.016112
aP.xyz 21 4536 0.001396 0.001407 0.019599 0.054174
aa.xyz 20 4320 0.001991 0.001991 0.016735 0.027955
iIn.xyz 41 8897 0.001548 0.001687 0.013910 0.025462
iP.xyz 100 21700 0.001090 0.001203 0.009692 0.018549
s_aIn.xyz 121 7744 0.000856 0.000889 0.011041 0.017399
s_aP.xyz 72 4608 0.002255 0.003587 0.032425 0.045878
s_aa.xyz 18 1152 0.001198 0.001200 0.037169 0.047713
s_iIn.xyz 144 9360 0.002014 0.002255 0.035374 0.050726
s_iP.xyz 337 21905 0.001655 0.002178 0.025130 0.038368
s_vIn.xyz 17 1071 0.007984 0.007992 0.023190 0.039575
s_vP.xyz 77 4851 0.000245 0.000281 0.018303 0.025819
s_vv.xyz 65 4030 0.001759 0.001986 0.039037 0.052667
vP.xyz 10 2150 0.000640 0.000640 0.005452 0.009834
vv.xyz 19 4066 0.001336 0.001403 0.020930 0.034386
--------------------------------------------------------------------------------------------
All files 1894 118214 0.001288 0.001855 0.018109 0.032649
--------------------------------------------------------------------------------------------
**************** End of Error Analysis for the Training Data Set ****************
Total wall time: 0:00:10

155
examples/PACKAGES/pod/InP/log.22May24.pod.g++.1 Normal file
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@ -0,0 +1,155 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Demonstrate POD potential for InP
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 5.83
units metal
# generate the box and atom positions using a FCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice diamond $a
lattice diamond 5.83
Lattice spacing in x,y,z = 5.83 5.83 5.83
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (23.32 23.32 23.32)
1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
Created 512 atoms
using lattice units in orthogonal box = (0 0 0) to (23.32 23.32 23.32)
create_atoms CPU = 0.001 seconds
mass 1 114.76
mass 2 30.98
# POD potential
pair_style pod
pair_coeff * * InP_param.pod InP_coefficients.pod In P
**************** Begin of POD Potentials ****************
species: In P
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 0.8
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 2
five-body radial basis functions: 0
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 12
number of local descriptors per element for three-body potential: 75
number of local descriptors per element for four-body potential: 64
number of local descriptors per element for five-body potential: 0
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 152
number of global descriptors: 304
**************** End of POD Potentials ****************
**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 304
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************
# Setup output
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6
ghost atom cutoff = 6
binsize = 3, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair pod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.244 | 3.244 | 3.244 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -4.8392777 0 -4.8005754 1561.0654
10 291.27079 -4.8381515 0 -4.8005753 1709.509
20 266.69372 -4.8349805 0 -4.8005749 2126.86
30 230.86163 -4.8303573 0 -4.8005744 2735.6894
40 190.64668 -4.8251686 0 -4.8005738 3416.9247
50 153.9516 -4.8204341 0 -4.8005732 4022.2533
60 127.93805 -4.8170778 0 -4.8005728 4405.9763
70 117.12501 -4.8156828 0 -4.8005727 4475.6131
80 122.09497 -4.8163242 0 -4.800573 4231.7934
90 139.42686 -4.8185607 0 -4.8005735 3766.8505
100 162.84813 -4.8215828 0 -4.8005741 3221.8605
Loop time of 2.18542 on 1 procs for 100 steps with 512 atoms
Performance: 1.977 ns/day, 12.141 hours/ns, 45.758 timesteps/s, 23.428 katom-step/s
97.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1829 | 2.1829 | 2.1829 | 0.0 | 99.88
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00080748 | 0.00080748 | 0.00080748 | 0.0 | 0.04
Output | 0.00033584 | 0.00033584 | 0.00033584 | 0.0 | 0.02
Modify | 0.00071224 | 0.00071224 | 0.00071224 | 0.0 | 0.03
Other | | 0.000686 | | | 0.03
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1451 ave 1451 max 1451 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 17408 ave 17408 max 17408 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17408
Ave neighs/atom = 34
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

155
examples/PACKAGES/pod/InP/log.22May24.pod.g++.4 Normal file
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@ -0,0 +1,155 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Demonstrate POD potential for InP
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 5.83
units metal
# generate the box and atom positions using a FCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice diamond $a
lattice diamond 5.83
Lattice spacing in x,y,z = 5.83 5.83 5.83
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 2 box
Created orthogonal box = (0 0 0) to (23.32 23.32 23.32)
1 by 2 by 2 MPI processor grid
create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
Created 512 atoms
using lattice units in orthogonal box = (0 0 0) to (23.32 23.32 23.32)
create_atoms CPU = 0.001 seconds
mass 1 114.76
mass 2 30.98
# POD potential
pair_style pod
pair_coeff * * InP_param.pod InP_coefficients.pod In P
**************** Begin of POD Potentials ****************
species: In P
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 0.8
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 2
five-body radial basis functions: 0
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 12
number of local descriptors per element for three-body potential: 75
number of local descriptors per element for four-body potential: 64
number of local descriptors per element for five-body potential: 0
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 152
number of global descriptors: 304
**************** End of POD Potentials ****************
**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 304
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************
# Setup output
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6
ghost atom cutoff = 6
binsize = 3, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair pod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.215 | 3.215 | 3.215 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -4.8392777 0 -4.8005754 1561.0654
10 291.27079 -4.8381515 0 -4.8005753 1709.509
20 266.69372 -4.8349805 0 -4.8005749 2126.86
30 230.86163 -4.8303573 0 -4.8005744 2735.6894
40 190.64668 -4.8251686 0 -4.8005738 3416.9247
50 153.9516 -4.8204341 0 -4.8005732 4022.2533
60 127.93805 -4.8170778 0 -4.8005728 4405.9763
70 117.12501 -4.8156828 0 -4.8005727 4475.6131
80 122.09497 -4.8163242 0 -4.800573 4231.7934
90 139.42686 -4.8185607 0 -4.8005735 3766.8505
100 162.84813 -4.8215828 0 -4.8005741 3221.8605
Loop time of 0.818141 on 4 procs for 100 steps with 512 atoms
Performance: 5.280 ns/day, 4.545 hours/ns, 122.228 timesteps/s, 62.581 katom-step/s
94.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.70717 | 0.7255 | 0.75748 | 2.2 | 88.68
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.05765 | 0.088203 | 0.10797 | 6.3 | 10.78
Output | 0.00030107 | 0.00039215 | 0.00055987 | 0.0 | 0.05
Modify | 0.00051915 | 0.00059064 | 0.00069306 | 0.0 | 0.07
Other | | 0.003452 | | | 0.42
Nlocal: 128 ave 128 max 128 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 783 ave 783 max 783 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4352 ave 4352 max 4352 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17408
Ave neighs/atom = 34
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

4
examples/PACKAGES/pod/Ta/README.md
View File

@ -5,11 +5,11 @@ of the training data taken from [the FitSNAP repo](https://github.com/FitSNAP/Fi
Fit POD with
lmp -in Ta_fit.pod
lmp -in in.fitpod
This creates `Ta_coefficients.pod` for the linear model, which we can use to run MD with
lmp -in Ta_mdrun.pod
lmp -in in.pod

5
examples/PACKAGES/pod/Ta/Ta_centroids.pod
View File

@ -1,5 +0,0 @@
centroids: 4
709.809117183618014
-87.224242759325506
290.052334466774596
-48.651919394376264

114
examples/PACKAGES/pod/Ta/Ta_coeff.pod
View File

@ -1,63 +1,63 @@
POD_coefficients: 62
-3.495093
-59.701906
30.663456
10.791538
0.840297
0.730228
0.910582
-67.196938
-179.985939
524.691284
670.837805
-259.035435
3.823252
52.397945
-63.764311
-120.411099
39.425094
1.642051
-10.593072
0.363492
16.232118
-2.165456
0.014326
0.691317
1.208074
-1.186301
-0.656701
model_coefficients: 62 0 0
-3.495092
-59.702301
30.663465
10.791500
0.840322
0.730233
0.910588
-67.197190
-179.980716
524.692031
670.830056
-259.034640
3.823282
52.396979
-63.764340
-120.409556
39.425007
1.642041
-10.592947
0.363512
16.231934
-2.165453
0.014335
0.691299
1.208040
-1.186298
-0.656703
0.011029
-0.044294
-0.042611
0.025912
0.025913
-0.035474
-5.179647
428.614009
-16.386364
126.893554
-410.027777
-953.238514
-18.330799
1.006988
-22.929962
-0.914978
-4.986332
29.072433
31.345932
0.723031
0.249736
-1.438448
-0.632864
0.148064
2.642487
-0.405224
0.104130
0.107113
-0.020909
-0.498780
0.247484
-5.168418
428.615879
-16.436190
126.897483
-410.022376
-953.258765
-18.282630
1.006650
-22.930080
-0.913472
-4.986589
29.072094
31.347224
0.721552
0.249755
-1.438459
-0.632951
0.148047
2.642466
-0.405122
0.104219
0.107115
-0.020907
-0.498791
0.247485
0.093056
-0.271642
0.355028
1.479538
-0.271639
0.355044
1.479539
-0.216955

114
examples/PACKAGES/pod/Ta/Ta_coefficients.pod
View File

@ -1,63 +1,63 @@
POD_coefficients: 62
-3.495093
-59.701906
30.663456
10.791538
0.840297
0.730228
0.910582
-67.196938
-179.985939
524.691284
670.837805
-259.035435
3.823252
52.397945
-63.764311
-120.411099
39.425094
1.642051
-10.593072
0.363492
16.232118
-2.165456
0.014326
0.691317
1.208074
-1.186301
-0.656701
model_coefficients: 62 0 0
-3.495092
-59.702301
30.663465
10.791500
0.840322
0.730233
0.910588
-67.197190
-179.980716
524.692031
670.830056
-259.034640
3.823282
52.396979
-63.764340
-120.409556
39.425007
1.642041
-10.592947
0.363512
16.231934
-2.165453
0.014335
0.691299
1.208040
-1.186298
-0.656703
0.011029
-0.044294
-0.042611
0.025912
0.025913
-0.035474
-5.179647
428.614009
-16.386364
126.893554
-410.027777
-953.238514
-18.330799
1.006988
-22.929962
-0.914978
-4.986332
29.072433
31.345932
0.723031
0.249736
-1.438448
-0.632864
0.148064
2.642487
-0.405224
0.104130
0.107113
-0.020909
-0.498780
0.247484
-5.168418
428.615879
-16.436190
126.897483
-410.022376
-953.258765
-18.282630
1.006650
-22.930080
-0.913472
-4.986589
29.072094
31.347224
0.721552
0.249755
-1.438459
-0.632951
0.148047
2.642466
-0.405122
0.104219
0.107115
-0.020907
-0.498791
0.247485
0.093056
-0.271642
0.355028
1.479538
-0.271639
0.355044
1.479539
-0.216955

123
examples/PACKAGES/pod/Ta/Ta_projection_matrix.pod
View File

@ -1,123 +0,0 @@
projection_matrix: 122
0.001542180493544
-0.000208856257237
0.004696325552750
-0.000799660184854
-0.008000933039354
0.001989066009842
0.010419332874197
-0.004225089382829
-0.007707874791396
0.002363181997412
0.000252747866160
0.001096501878869
0.002521274077638
0.001255396173484
0.000003198549918
-0.000001703803015
0.000842660980413
0.000418209680165
0.000003061593770
-0.000001369337964
0.000513414778155
0.000251234560810
0.022147135061506
0.008240622324666
0.000028539708383
-0.000015268759157
0.007398308113533
0.002742126611657
0.000026507655563
-0.000012826875616
0.004500875045773
0.001633854036062
0.057992487693725
0.004399845607684
0.000087830232758
-0.000047234108179
0.019371949049613
0.001446775035292
0.000080198873386
-0.000042979676692
0.011803130149159
0.000782571344815
0.088729781220177
-0.033994314705254
0.000137177658945
-0.000074274009518
0.029695365361865
-0.011332825206724
0.000122060283043
-0.000052535526824
0.018045534605097
-0.006782004476568
0.055582489447206
0.003772200119617
0.000646578781880
-0.000349051715974
0.019370224642909
0.000987429380699
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726
examples/PACKAGES/pod/Ta/Ta_training_analysis.pod
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@ -1,387 +1,387 @@
# Displaced_A15.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
1 64 1191.016129 -754.239768 -754.220443 0.0003019536715 7.114871757 8.398670477 0.1695557832
2 64 1191.016129 -753.7481488 -753.865255 0.001829784368 8.386710671 9.134430545 0.1759889315
3 64 1191.016129 -754.1045865 -754.0221 0.001288852097 7.745893493 9.017261102 0.1535051337
4 64 1191.016129 -754.3352492 -754.279613 0.0008693163237 7.141398358 8.381725092 0.1470272165
5 64 1191.016129 -753.7390488 -753.777209 0.0005962536982 8.559864212 9.478314477 0.1599737353
6 64 1191.016129 -754.1350606 -754.048643 0.001350275659 7.125973492 8.465317938 0.1492137965
7 64 1191.016129 -754.3192932 -754.317603 2.640994023e-05 7.146736476 8.127690491 0.1293428957
8 64 1191.016129 -754.0300838 -753.969161 0.0009519190691 8.306786503 9.425464952 0.144726961
9 64 1191.016129 -754.1789472 -754.141988 0.0005774880456 7.589147667 8.821346913 0.1562251608
1 64 1191.016129 -754.2397656 -754.220443 0.0003019162109 7.114876401 8.398670477 0.1695551671
2 64 1191.016129 -753.748147 -753.865255 0.001829812752 8.386711581 9.134430545 0.1759882337
3 64 1191.016129 -754.1045834 -754.0221 0.001288803613 7.745899298 9.017261102 0.153504591
4 64 1191.016129 -754.3352478 -754.279613 0.0008692941345 7.141398255 8.381725092 0.1470268434
5 64 1191.016129 -753.7390466 -753.777209 0.0005962881977 8.559866206 9.478314477 0.1599730259
6 64 1191.016129 -754.1350584 -754.048643 0.001350241245 7.125978347 8.465317938 0.1492132373
7 64 1191.016129 -754.3192913 -754.317603 2.637930836e-05 7.146739834 8.127690491 0.129342387
8 64 1191.016129 -754.0300816 -753.969161 0.000951884558 8.306788612 9.425464952 0.1447265722
9 64 1191.016129 -754.1789439 -754.141988 0.0005774365826 7.589153887 8.821346913 0.1562245793
# Displaced_BCC.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
10 54 988.0479474 -630.9511271 -631.019667 0.001269257072 16.45090046 16.625876 0.2011388903
11 54 988.0479474 -631.6415899 -631.719595 0.00144453882 15.52807832 15.58666626 0.2008905704
12 54 988.0479474 -631.1690717 -631.386255 0.004021913114 16.05429981 15.92378883 0.1885050869
13 54 988.0479474 -632.5637097 -632.575826 0.0002243754829 14.58341036 14.55977162 0.1840867908
14 54 988.0479474 -630.128723 -630.450212 0.005953500291 17.4135469 16.96340726 0.2004262579
15 54 988.0479474 -631.5496733 -631.669379 0.002216771672 15.93055416 16.05757315 0.1985387875
16 54 988.0479474 -632.2011582 -632.431277 0.004261460157 15.15844179 14.69810718 0.193025243
17 54 988.0479474 -630.8938576 -630.960068 0.001226119006 16.03733229 15.99073148 0.1838781855
18 54 988.0479474 -623.635469 -623.378198 0.004764277831 24.0443294 24.67640432 0.2554135698
10 54 988.0479474 -630.9511261 -631.019667 0.001269276034 16.45090713 16.625876 0.2011388281
11 54 988.0479474 -631.641588 -631.719595 0.001444574941 15.52808613 15.58666626 0.2008906391
12 54 988.0479474 -631.1690748 -631.386255 0.004021855057 16.0542988 15.92378883 0.1885049544
13 54 988.0479474 -632.5637117 -632.575826 0.0002243395026 14.58340738 14.55977162 0.1840868116
14 54 988.0479474 -630.1287203 -630.450212 0.0059535492 17.41355771 16.96340726 0.2004264556
15 54 988.0479474 -631.5496743 -631.669379 0.00221675308 15.93054994 16.05757315 0.1985385249
16 54 988.0479474 -632.2011601 -632.431277 0.004261423789 15.15844111 14.69810718 0.1930251239
17 54 988.0479474 -630.8938569 -630.960068 0.001226132075 16.03733469 15.99073148 0.1838780138
18 54 988.0479474 -623.6354728 -623.378198 0.004764347947 24.04431721 24.67640432 0.2554142506
# Displaced_FCC.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
19 48 889.0559462 -555.9736438 -555.899463 0.001545434108 5.381668461 6.084617063 0.07848426343
20 48 889.0559462 -555.9807201 -555.922478 0.001213376388 5.492407199 6.297071211 0.09272626513
21 48 889.0559462 -555.8362146 -555.800269 0.0007488667685 5.538971182 6.021098636 0.08165961852
22 48 889.0559462 -556.221859 -556.196151 0.0005355828547 4.650599881 5.127955094 0.06983880934
23 48 889.0559462 -555.5903634 -555.488929 0.002113216964 6.316246126 7.050223459 0.09863942093
24 48 889.0559462 -556.054531 -556.027926 0.0005542705749 5.144372144 5.611881174 0.07532849334
25 48 889.0559462 -556.042969 -555.968399 0.001553542708 5.256474014 5.979217189 0.09018814209
26 48 889.0559462 -556.0476229 -556.047132 1.02264757e-05 5.022262418 5.544452585 0.08281260893
27 48 889.0559462 -555.7888733 -555.747848 0.0008546946787 5.875149824 6.47892568 0.09188021396
19 48 889.0559462 -555.9736421 -555.899463 0.001545398294 5.381675728 6.084617063 0.07848404605
20 48 889.0559462 -555.9807188 -555.922478 0.001213349709 5.492413853 6.297071211 0.09272601944
21 48 889.0559462 -555.836213 -555.800269 0.0007488324191 5.538978887 6.021098636 0.08165922907
22 48 889.0559462 -556.2218582 -556.196151 0.0005355671902 4.650604248 5.127955094 0.06983864474
23 48 889.0559462 -555.5903622 -555.488929 0.002113191361 6.316251166 7.050223459 0.09863914436
24 48 889.0559462 -556.0545299 -556.027926 0.0005542488903 5.144377449 5.611881174 0.07532829079
25 48 889.0559462 -556.0429677 -555.968399 0.001553514764 5.256481083 5.979217189 0.0901877504
26 48 889.0559462 -556.0476215 -556.047132 1.019871101e-05 5.022268768 5.544452585 0.08281227892
27 48 889.0559462 -555.7888725 -555.747848 0.0008546766621 5.875154209 6.47892568 0.0918800737
# Elastic_BCC.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
28 2 36.40799882 -23.68982108 -23.689367 0.0002270388554 0.0006173153829 0.0006222748589 3.412818336e-06
29 2 36.47727251 -23.68983848 -23.689888 2.476046779e-05 0.0006122766086 0.0006166052222 2.590948112e-06
30 2 36.47184897 -23.68986593 -23.689996 6.503296041e-05 0.0008746372027 0.0008810425642 3.663849801e-06
31 2 36.62078348 -23.68949555 -23.690957 0.0007307236292 9.939434046e-07 0 3.979601123e-07
32 2 36.71197042 -23.68851035 -23.690521 0.001005322968 0.0005927165677 0.0005982273815 2.567190505e-06
33 2 36.77593928 -23.68767046 -23.69038 0.001354770373 0.0005881581552 0.0005925723585 2.074338215e-06
34 2 36.36547558 -23.69007983 -23.689202 0.0004389148547 0.0006209499378 0.0006279363025 3.498534274e-06
35 2 36.55974375 -23.6893557 -23.690482 0.0005631515421 0.0008538422052 0.0008640138888 4.527563009e-06
36 2 36.46414346 -23.68988711 -23.689902 7.445386322e-06 0.0006119039538 0.0006152154094 2.513558215e-06
37 2 36.63368821 -23.6891908 -23.690563 0.0006860985596 0.0005988489701 0.0006038725031 1.535212865e-06
38 2 36.45345189 -23.69010693 -23.690207 5.003532698e-05 0.001061291046 0.00107369735 5.06572008e-06
39 2 36.38484847 -23.68957173 -23.689285 0.0001433642278 0.0008814788535 0.000890013483 3.2395313e-06
40 2 36.43347895 -23.69002647 -23.689768 0.0001292329849 0.001070807691 0.001080249045 3.872098934e-06
41 2 36.50220719 -23.68945911 -23.68968 0.0001104459034 0.0008614661229 0.0008680034562 2.221301856e-06
42 2 36.50719109 -23.69010485 -23.690074 1.54229661e-05 0.001350139768 0.001373818765 1.143299054e-05
43 2 36.28428565 -23.68987699 -23.688108 0.0008844971239 0.0006287345635 0.0006336134468 3.327703961e-06
44 2 36.3642236 -23.6897877 -23.689241 0.0002733495724 0.0008826646412 0.0008880101351 1.858037344e-06
45 2 36.40397469 -23.69027117 -23.68952 0.0003755829434 0.0008819306622 0.0008860011287 1.360861965e-06
46 2 36.15958616 -23.68916607 -23.686278 0.001444035119 0.0006386357241 0.0006406777661 2.822539456e-06
47 2 36.85012426 -23.68683466 -23.690097 0.001631171409 0.0008336956895 0.0008410160522 2.498295917e-06
48 2 36.76983294 -23.68825449 -23.690811 0.001278255347 0.0008379337186 0.0008500070588 5.057356677e-06
49 2 36.6630398 -23.68853268 -23.690266 0.0008666581824 0.001023710406 0.001044322747 8.430320373e-06
50 2 36.55357619 -23.6899612 -23.690597 0.000317901365 0.001025967982 0.001050833003 1.015083269e-05
51 2 36.65271066 -23.6894166 -23.690673 0.0006282018963 0.0005979605296 0.0006038907186 3.12740275e-06
52 2 36.56222224 -23.68973914 -23.690551 0.0004059293245 0.0008407335956 0.0008590064028 6.29059838e-06
53 2 36.56679849 -23.68989374 -23.690693 0.0003996320113 0.0008422878383 0.0008590110593 6.333586427e-06
54 2 36.59811665 -23.68914708 -23.69021 0.0005314600536 0.0008647500677 0.0008730051546 3.307551172e-06
55 2 36.34900278 -23.69007909 -23.688943 0.0005680454734 0.000866623272 0.0008800306813 5.954163747e-06
56 2 36.74034826 -23.687958 -23.690136 0.001088999378 0.0005907684978 0.000593996633 1.944369951e-06
57 2 36.23610366 -23.68963551 -23.687444 0.001095755533 0.0009013711162 0.000903059245 2.714217201e-06
58 2 36.42259639 -23.69011147 -23.689801 0.0001552343944 0.0008616813923 0.0008740011442 4.417412809e-06
59 2 36.58194 -23.68962541 -23.690408 0.0003912950897 8.183432434e-07 0 3.052045111e-07
60 2 36.59950783 -23.68950464 -23.690362 0.0004286821837 0.0006021519367 0.0006067503605 3.453501663e-06
61 2 37.02589653 -23.68476757 -23.688881 0.002056715854 0.0008110538156 0.0008250054545 5.595917398e-06
62 2 36.71189602 -23.68839354 -23.690515 0.001060729297 0.001462829059 0.001475779794 5.735804376e-06
63 2 36.78962367 -23.68800936 -23.690551 0.001270819535 0.0005878817141 0.0005996599036 4.322952812e-06
64 2 36.42642467 -23.68946784 -23.689487 9.581705156e-06 0.0006155193688 0.0006194384554 2.471891908e-06
65 2 36.4423543 -23.69013635 -23.68986 0.0001381765763 0.0008827248932 0.0008860124153 1.742424392e-06
66 2 36.39164409 -23.68994443 -23.689288 0.0003282147053 0.001391934594 0.001396479144 1.512281983e-06
67 2 36.83059874 -23.68751455 -23.690457 0.001471222827 0.0005838782045 0.0005939831647 4.000156387e-06
68 2 36.8936692 -23.68679934 -23.689792 0.001496332092 0.0008138408917 0.0008340587509 9.248007837e-06
69 2 36.88495742 -23.6870374 -23.690006 0.001484299175 0.0005799611936 0.0005897694465 4.668214423e-06
70 2 36.7928657 -23.68783289 -23.690571 0.001369053939 0.0005864446896 0.0005939781141 3.119322479e-06
71 2 36.50844234 -23.69025387 -23.690213 2.043307459e-05 0.001087009003 0.001084315452 1.095983692e-06
72 2 36.74419477 -23.68837262 -23.690617 0.001122187668 0.0005904477851 0.0006024682564 3.852148718e-06
73 2 36.49448266 -23.68936822 -23.689761 0.0001963922799 0.0008741817944 0.0008790688255 3.754672595e-06
74 2 36.83933705 -23.68732648 -23.69027 0.001471758804 6.853576005e-07 0 2.049427721e-07
75 2 36.5709148 -23.68949725 -23.690599 0.000550876114 0.0006042094999 0.0006137752031 2.806846094e-06
76 2 36.67683082 -23.68905345 -23.69061 0.0007782757965 9.039582285e-07 0 3.689274687e-07
77 2 36.66115635 -23.68881909 -23.690603 0.0008919537446 0.0008443856837 0.0008590331775 5.777019964e-06
78 2 36.25583797 -23.68966161 -23.687908 0.0008768073253 0.0009027129535 0.0009010105438 1.519707511e-06
79 2 36.69315685 -23.6884904 -23.690688 0.00109880125 0.000833655946 0.0008470064935 5.213466962e-06
80 2 36.46769977 -23.69025919 -23.689988 0.0001355936519 0.0006132993083 0.0006194465272 3.498929034e-06
81 2 36.44434113 -23.68998504 -23.689613 0.0001860187586 0.0008647359851 0.0008740732235 5.784809823e-06
82 2 36.57453003 -23.68991497 -23.690678 0.0003815172499 0.0006042929299 0.0006123757017 3.579463209e-06
83 2 36.54218785 -23.68969209 -23.69017 0.0002389570014 0.0008646207347 0.0008750051428 3.584519606e-06
84 2 36.26350252 -23.68977897 -23.687892 0.0009434874404 0.00111721459 0.001112070142 2.099077156e-06
85 2 36.49725495 -23.69000301 -23.690132 6.449427224e-05 0.0008483115993 0.000868018433 7.609453431e-06
86 2 36.66468316 -23.68895566 -23.690843 0.0009436720969 0.000596266669 0.0006081134763 3.60300613e-06
87 2 36.69098146 -23.68863331 -23.690598 0.0009823430881 0.001190611035 0.001217674833 1.00339027e-05
88 2 36.7498524 -23.68848668 -23.690656 0.001084659436 0.0005906599393 0.0006024765556 4.413107056e-06
89 2 36.72620595 -23.68835653 -23.690254 0.0009487342974 0.001027915429 0.001043496047 6.729807619e-06
90 2 36.7046344 -23.6890565 -23.690694 0.0008187486436 0.0005936130323 0.0006010740387 3.384838827e-06
91 2 36.53215524 -23.68956015 -23.690097 0.0002684229092 0.0008698237518 0.0008730234819 2.171567134e-06
92 2 36.28988463 -23.68992826 -23.688402 0.000763130351 0.0006274188299 0.000632180354 2.59528116e-06
93 2 36.330155 -23.6897505 -23.688669 0.0005407489059 0.001086304971 0.001092474256 2.70574859e-06
94 2 36.65451876 -23.68888484 -23.690538 0.0008265808998 0.0008468906751 0.0008610145179 4.729527723e-06
95 2 36.46623662 -23.68985976 -23.689722 6.887867969e-05 0.0006144576043 0.0006251287867 4.354052528e-06
96 2 36.73431174 -23.68861477 -23.690581 0.0009831134723 7.042873074e-07 0 2.230378477e-07
97 2 36.34544239 -23.6897464 -23.688755 0.0004957018965 0.0006216312954 0.0006251143895 2.669360327e-06
98 2 36.9736935 -23.68573067 -23.689312 0.001790663349 0.0008166045347 0.0008290597083 6.258297673e-06
99 2 36.24487417 -23.68982786 -23.687388 0.001219932196 0.00113422659 0.001120237475 5.712296431e-06
100 2 36.57555586 -23.68980457 -23.690664 0.0004297171556 0.0006037015015 0.0006109402589 1.751753805e-06
101 2 36.94151938 -23.68639201 -23.68941 0.001508997377 0.0005769935199 0.0005883553348 5.341569129e-06
102 2 36.45547212 -23.68995114 -23.690035 4.192916492e-05 0.0008734653786 0.0008810062429 2.735257238e-06
103 2 36.88496132 -23.68704123 -23.690015 0.001486887176 0.000836497392 0.0008450195264 4.240650299e-06
104 2 36.76103389 -23.68848604 -23.690752 0.001132979447 0.0005899803825 0.0005996415596 3.598896446e-06
105 2 36.45404349 -23.68958624 -23.689825 0.0001193793821 0.0008697491142 0.0008800215906 3.799260971e-06
106 2 36.74654739 -23.68860785 -23.690562 0.0009770746684 0.0008454786194 0.0008560011682 3.733348001e-06
107 2 36.74084732 -23.68835546 -23.690622 0.001133272329 0.0008209873728 0.0008390017878 6.251000245e-06
108 2 36.33025646 -23.68986236 -23.688764 0.0005491777774 0.0008888925985 0.0008910185183 2.17332635e-06
109 2 36.44122368 -23.68996666 -23.690011 2.216977164e-05 0.0006144987893 0.0006194287691 1.534217402e-06
110 2 36.25348342 -23.68951809 -23.687696 0.0009110453712 0.00106948221 0.001087589996 7.391851899e-06
111 2 36.69693588 -23.68894311 -23.691019 0.001037945304 0.0008428255952 0.0008540035129 4.290318122e-06
112 2 36.3425194 -23.69010839 -23.689025 0.0005416940188 6.441401309e-07 0 2.542974732e-07
113 2 36.51656499 -23.6893838 -23.689952 0.0002840998321 6.950152607e-07 0 2.727911313e-07
114 2 36.71447816 -23.68887269 -23.69061 0.0008686545341 0.0008467945855 0.0008580011655 4.176015257e-06
115 2 36.62519495 -23.68972206 -23.690595 0.0004364722545 0.0008643051678 0.0008680069124 1.566974163e-06
116 2 36.80154127 -23.68768352 -23.690231 0.001273737991 0.0005856460415 0.0005925892338 3.06485662e-06
117 2 36.77742539 -23.68818518 -23.690469 0.0011419116 0.000842615541 0.0008500294113 3.854363961e-06
118 2 36.50183296 -23.69003768 -23.690482 0.0002221616947 0.000866528807 0.0008740102974 3.157426634e-06
119 2 36.93568763 -23.68590485 -23.689613 0.001854074182 0.0008101552543 0.0008320192305 8.354516214e-06
120 2 36.23289183 -23.68971904 -23.687426 0.001146519954 0.00108025617 0.00109577735 6.360023182e-06
121 2 36.44295904 -23.68957777 -23.689562 7.887098224e-06 0.0006153253615 0.0006265237426 3.930028944e-06
122 2 36.59751671 -23.68979901 -23.6904 0.0003004968343 3.82089167e-07 0 1.551082178e-07
123 2 36.76766724 -23.68854201 -23.690561 0.001009494544 0.000589264154 0.0005982273815 3.926880128e-06
124 2 37.00025894 -23.68511902 -23.689107 0.001993990094 0.0007962791576 0.0008180073349 7.883394774e-06
125 2 36.58722353 -23.68944636 -23.690145 0.0003493219608 0.0008715131438 0.0008740766557 3.795931368e-06
126 2 36.79405605 -23.68800403 -23.690482 0.0012389853 0.000587415399 0.0005939983165 2.772075495e-06
127 2 36.45320348 -23.68995365 -23.689864 4.482387553e-05 0.0008821697844 0.0008860124153 2.264741356e-06
28 2 36.40799882 -23.68982109 -23.689367 0.0002270452993 0.0006173158802 0.0006222748589 3.412727734e-06
29 2 36.47727251 -23.68983849 -23.689888 2.475513559e-05 0.0006122770598 0.0006166052222 2.590858461e-06
30 2 36.47184897 -23.68986594 -23.689996 6.502766776e-05 0.0008746379172 0.0008810425642 3.663633668e-06
31 2 36.62078348 -23.68949556 -23.690957 0.0007307211124 9.939440467e-07 0 3.979603704e-07
32 2 36.71197042 -23.68851036 -23.690521 0.001005321597 0.0005927168699 0.0005982273815 2.567135089e-06
33 2 36.77593928 -23.68767046 -23.69038 0.001354770119 0.0005881584179 0.0005925723585 2.074286875e-06
34 2 36.36547558 -23.69007984 -23.689202 0.000438921832 0.0006209504668 0.0006279363025 3.498430822e-06
35 2 36.55974375 -23.6893557 -23.690482 0.0005631477446 0.0008538427608 0.0008640138888 4.527390089e-06
36 2 36.46414346 -23.68988712 -23.689902 7.439928606e-06 0.0006119044068 0.0006152154094 2.513477408e-06
37 2 36.63368821 -23.68919081 -23.690563 0.0006860958985 0.0005988493185 0.0006038725031 1.535139148e-06
38 2 36.45345189 -23.69010694 -23.690207 5.00299988e-05 0.001061291854 0.00107369735 5.065390367e-06
39 2 36.38484847 -23.68957174 -23.689285 0.0001433709104 0.0008814796217 0.000890013483 3.239283078e-06
40 2 36.43347895 -23.69002648 -23.689768 0.0001292388775 0.001070808568 0.001080249045 3.8717412e-06
41 2 36.50220719 -23.68945912 -23.68968 0.0001104407207 0.0008614667308 0.0008680034562 2.221102274e-06
42 2 36.50719109 -23.69010486 -23.690074 1.542781836e-05 0.001350140656 0.001373818765 1.14327725e-05
43 2 36.28428565 -23.68987701 -23.688108 0.0008845055232 0.0006287351502 0.0006336134468 3.327595276e-06
44 2 36.3642236 -23.68978771 -23.689241 0.0002733564815 0.0008826654177 0.0008880101351 1.857781948e-06
45 2 36.40397469 -23.69027118 -23.68952 0.0003755893452 0.000881931427 0.0008860011287 1.360603975e-06
46 2 36.15958616 -23.68916609 -23.686278 0.001444045375 0.0006386363881 0.0006406777661 2.82241612e-06
47 2 36.85012426 -23.68683466 -23.690097 0.001631172479 0.0008336960828 0.0008410160522 2.498167338e-06
48 2 36.76983294 -23.68825449 -23.690811 0.001278255357 0.0008379341582 0.0008500070588 5.057221377e-06
49 2 36.6630398 -23.68853269 -23.690266 0.0008666557629 0.001023710931 0.001044322747 8.430106501e-06
50 2 36.55357619 -23.6899612 -23.690597 0.0003178975626 0.001025968529 0.001050833003 1.015060901e-05
51 2 36.65271066 -23.6894166 -23.690673 0.0006281996224 0.0005979608736 0.0006038907186 3.127344339e-06
52 2 36.56222224 -23.68973915 -23.690551 0.0004059255931 0.0008407340638 0.0008590064028 6.290446869e-06
53 2 36.56679849 -23.68989374 -23.690693 0.0003996284571 0.0008422883199 0.0008590110593 6.333438683e-06
54 2 36.59811665 -23.68914709 -23.69021 0.0005314565537 0.0008647507078 0.0008730051546 3.307345991e-06
55 2 36.34900278 -23.69007911 -23.688943 0.000568052776 0.0008666239395 0.0008800306813 5.953964641e-06
56 2 36.74034826 -23.687958 -23.690136 0.001088998168 0.0005907687786 0.000593996633 1.944321518e-06
57 2 36.23610366 -23.68963553 -23.687444 0.001095764653 0.0009013720355 0.000903059245 2.714243395e-06
58 2 36.42259639 -23.69011148 -23.689801 0.0001552403771 0.0008616820143 0.0008740011442 4.417209346e-06
59 2 36.58194 -23.68962542 -23.690408 0.0003912914995 8.183437702e-07 0 3.052047089e-07
60 2 36.59950783 -23.68950464 -23.690362 0.0004286788156 0.0006021523109 0.0006067503605 3.453449156e-06
61 2 37.02589653 -23.68476756 -23.688881 0.002056720162 0.0008110540502 0.0008250054545 5.5958497e-06
62 2 36.71189602 -23.68839354 -23.690515 0.00106072795 0.001462829888 0.001475779794 5.735697599e-06
63 2 36.78962367 -23.68800936 -23.690551 0.001270819695 0.000587881995 0.0005996599036 4.322910641e-06
64 2 36.42642467 -23.68946785 -23.689487 9.575570509e-06 0.0006155198483 0.0006194384554 2.471797359e-06
65 2 36.4423543 -23.69013636 -23.68986 0.0001381823141 0.0008827256685 0.0008860124153 1.742177894e-06
66 2 36.39164409 -23.68994444 -23.689288 0.0003282213758 0.001391935777 0.001396479144 1.511902819e-06
67 2 36.83059874 -23.68751455 -23.690457 0.001471223786 0.0005838784492 0.0005939831647 4.000118713e-06
68 2 36.8936692 -23.68679933 -23.689792 0.001496333849 0.0008138411554 0.0008340587509 9.24795367e-06
69 2 36.88495742 -23.6870374 -23.690006 0.001484300932 0.0005799614079 0.0005897694465 4.668195862e-06
70 2 36.7928657 -23.68783289 -23.690571 0.001369054197 0.0005864449494 0.0005939781141 3.119271499e-06
71 2 36.50844234 -23.69025388 -23.690213 2.043781977e-05 0.00108700997 0.001084315452 1.096378417e-06
72 2 36.74419477 -23.68837263 -23.690617 0.001122186992 0.0005904480896 0.0006024682564 3.852092946e-06
73 2 36.49448266 -23.68936823 -23.689761 0.0001963870835 0.0008741824997 0.0008790688255 3.754690341e-06
74 2 36.83933705 -23.68732648 -23.69027 0.001471759777 6.853578862e-07 0 2.049428609e-07
75 2 36.5709148 -23.68949725 -23.690599 0.0005508725659 0.0006042099038 0.0006137752031 2.806761331e-06
76 2 36.67683082 -23.68905345 -23.69061 0.0007782738739 9.039586461e-07 0 3.689276393e-07
77 2 36.66115635 -23.6888191 -23.690603 0.0008919515963 0.0008443861786 0.0008590331775 5.776871513e-06
78 2 36.25583797 -23.68966163 -23.687908 0.0008768159977 0.0009027138709 0.0009010105438 1.520026907e-06
79 2 36.69315685 -23.6884904 -23.690688 0.00109879973 0.0008336563471 0.0008470064935 5.213340053e-06
80 2 36.46769977 -23.6902592 -23.689988 0.0001355990502 0.0006132997721 0.0006194465272 3.498843403e-06
81 2 36.44434113 -23.68998505 -23.689613 0.0001860246785 0.000864736624 0.0008740732235 5.784633772e-06
82 2 36.57453003 -23.68991497 -23.690678 0.0003815137832 0.0006042933274 0.0006123757017 3.579391974e-06
83 2 36.54218785 -23.68969209 -23.69017 0.0002389526975 0.0008646213816 0.0008750051428 3.584304313e-06
84 2 36.26350252 -23.68977899 -23.687892 0.0009434960918 0.001117215799 0.001112070142 2.099570806e-06
85 2 36.49725495 -23.69000302 -23.690132 6.448935551e-05 0.000848312132 0.000868018433 7.609293687e-06
86 2 36.66468316 -23.68895566 -23.690843 0.0009436702065 0.0005962670189 0.0006081134763 3.602933525e-06
87 2 36.69098146 -23.68863332 -23.690598 0.0009823414382 0.001190611721 0.001217674833 1.003378532e-05
88 2 36.7498524 -23.68848668 -23.690656 0.001084658895 0.0005906602407 0.0006024765556 4.413059545e-06
89 2 36.72620595 -23.68835653 -23.690254 0.0009487329348 0.001027915974 0.001043496047 6.729765279e-06
90 2 36.7046344 -23.68905651 -23.690694 0.0008187472736 0.0005936133477 0.0006010740387 3.384788947e-06
91 2 36.53215524 -23.68956016 -23.690097 0.0002684184124 0.0008698244171 0.0008730234819 2.17136251e-06
92 2 36.28988463 -23.68992828 -23.688402 0.0007631384698 0.0006274194068 0.000632180354 2.595167723e-06
93 2 36.330155 -23.68975051 -23.688669 0.0005407565174 0.001086305962 0.001092474256 2.705626249e-06
94 2 36.65451876 -23.68888484 -23.690538 0.0008265785841 0.000846891191 0.0008610145179 4.729354993e-06
95 2 36.46623662 -23.68985977 -23.689722 6.888426729e-05 0.0006144580845 0.0006251287867 4.353968594e-06
96 2 36.73431174 -23.68861477 -23.690581 0.0009831125559 7.042876594e-07 0 2.230379484e-07
97 2 36.34544239 -23.68974642 -23.688755 0.0004957093422 0.0006216318258 0.0006251143895 2.669261963e-06
98 2 36.9736935 -23.68573067 -23.689312 0.001790666627 0.0008166048055 0.0008290597083 6.258238489e-06
99 2 36.24487417 -23.68982788 -23.687388 0.00121994135 0.001134227905 0.001120237475 5.712833522e-06
100 2 36.57555586 -23.68980457 -23.690664 0.0004297137004 0.0006037018931 0.0006109402589 1.751662938e-06
101 2 36.94151938 -23.686392 -23.68941 0.001508999884 0.0005769937143 0.0005883553348 5.341556531e-06
102 2 36.45547212 -23.68995115 -23.690035 4.192373289e-05 0.0008734660897 0.0008810062429 2.735024749e-06
103 2 36.88496132 -23.68704122 -23.690015 0.001486888924 0.0008364978123 0.0008450195264 4.240529079e-06
104 2 36.76103389 -23.68848604 -23.690752 0.001132979204 0.0005899806736 0.0005996415596 3.598844352e-06
105 2 36.45404349 -23.68958625 -23.689825 0.0001193737946 0.0008697497974 0.0008800215906 3.799037847e-06
106 2 36.74654739 -23.68860785 -23.690562 0.0009770739717 0.000845479109 0.0008560011682 3.733189013e-06
107 2 36.74084732 -23.68835546 -23.690622 0.00113327162 0.000820987689 0.0008390017878 6.250899881e-06
108 2 36.33025646 -23.68986237 -23.688764 0.0005491853469 0.0008888934158 0.0008910185183 2.173072722e-06
109 2 36.44122368 -23.68996667 -23.690011 2.216417916e-05 0.0006144992641 0.0006194287691 1.534113774e-06
110 2 36.25348342 -23.68951811 -23.687696 0.0009110542045 0.001069483089 0.001087589996 7.391492952e-06
111 2 36.69693588 -23.68894311 -23.691019 0.001037944115 0.0008428260679 0.0008540035129 4.290165691e-06
112 2 36.3425194 -23.6901084 -23.689025 0.0005417013042 6.44140738e-07 0 2.5429771e-07
113 2 36.51656499 -23.68938381 -23.689952 0.000284095055 6.950158278e-07 0 2.72791348e-07
114 2 36.71447816 -23.68887269 -23.69061 0.0008686532809 0.0008467950921 0.0008580011655 4.1758523e-06
115 2 36.62519495 -23.68972206 -23.690595 0.0004364694647 0.0008643057932 0.0008680069124 1.566772283e-06
116 2 36.80154127 -23.68768352 -23.690231 0.001273738105 0.0005856462931 0.0005925892338 3.064822782e-06
117 2 36.77742539 -23.68818518 -23.690469 0.001141911429 0.0008426160012 0.0008500294113 3.854232399e-06
118 2 36.50183296 -23.69003769 -23.690482 0.0002221571341 0.00086652946 0.0008740102974 3.157220449e-06
119 2 36.93568763 -23.68590485 -23.689613 0.001854076824 0.0008101555003 0.0008320192305 8.354451123e-06
120 2 36.23289183 -23.68971906 -23.687426 0.001146529123 0.001080257131 0.00109577735 6.359631497e-06
121 2 36.44295904 -23.68957779 -23.689562 7.893027814e-06 0.0006153258576 0.0006265237426 3.929932717e-06
122 2 36.59751671 -23.68979901 -23.6904 0.0003004934568 3.820893957e-07 0 1.551083114e-07
123 2 36.76766724 -23.68854201 -23.690561 0.00100949424 0.0005892644358 0.0005982273815 3.926831901e-06
124 2 37.00025894 -23.68511901 -23.689107 0.001993993911 0.0007962792904 0.0008180073349 7.883360379e-06
125 2 36.58722353 -23.68944636 -23.690145 0.000349318232 0.0008715138165 0.0008740766557 3.795954855e-06
126 2 36.79405605 -23.68800403 -23.690482 0.001238985486 0.0005874156599 0.0005939983165 2.77203557e-06
127 2 36.45320348 -23.68995366 -23.689864 4.482948312e-05 0.0008821705514 0.0008860124153 2.264499306e-06
# Elastic_FCC.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
128 4 74.14589882 -46.43773689 -46.437936 4.977815948e-05 0.0007580066189 0.001265949446 0.0001549131423
129 4 74.26852111 -46.44163803 -46.438504 0.0007835074437 0.0007928720883 0.001492549497 0.0001864508395
130 4 74.05957274 -46.4350456 -46.436378 0.0003330997819 0.000501044284 0.000810592376 0.0001083763002
131 4 74.30647158 -46.44214695 -46.441551 0.0001489870341 0.0009248092827 0.001283675193 0.0001072336149
132 4 73.40902276 -46.41147986 -46.416957 0.001369284989 0.0008054001207 0.001186145859 0.0001080528493
133 4 74.1804881 -46.43910949 -46.440495 0.0003463787413 0.000800204383 0.001212440514 9.528548943e-05
134 4 74.17596744 -46.43848913 -46.437972 0.0001292826398 0.001183921951 0.002358226452 0.0002970857553
135 4 74.73528136 -46.45170359 -46.44586 0.001460897807 0.001133139927 0.002033949852 0.0002537826227
136 4 74.0787509 -46.43566767 -46.435744 1.908321455e-05 0.0008616099543 0.001690849491 0.0002669029292
137 4 74.24609528 -46.44080155 -46.438209 0.0006481386515 0.0007503721813 0.001160049999 9.912555662e-05
138 4 73.73005434 -46.42419117 -46.42629 0.0005247076028 0.000497639383 0.0005297018029 1.25837436e-05
139 4 74.33993289 -46.44322431 -46.443301 1.917309022e-05 0.0009242730465 0.001818421568 0.0002230025019
140 4 74.20715045 -46.43973494 -46.439002 0.0001832354738 0.001024144469 0.001416973535 0.0001023493877
141 4 73.89686848 -46.43019549 -46.432438 0.0005606275627 0.00096388637 0.001010469198 5.94739056e-05
142 4 73.27773838 -46.40573762 -46.412654 0.001729095774 0.001208978707 0.001801959766 0.0001722767373
143 4 74.40027968 -46.44461577 -46.443231 0.0003461920468 0.0007381689367 0.001691590967 0.0002039522371
144 4 73.86123747 -46.42927594 -46.431513 0.0005592656279 0.001235983419 0.001680544852 0.0001101435619
145 4 73.96908649 -46.43260512 -46.435608 0.0007507189852 0.0007552776734 0.0009593039143 4.83602511e-05
146 4 74.18717232 -46.43958279 -46.437689 0.000473446608 0.0007940421745 0.001217708504 0.0001255349732
147 4 73.76897316 -46.42538038 -46.428447 0.0007666541906 0.0009193515852 0.002060081552 0.0002986537405
148 4 73.9161373 -46.43089812 -46.432255 0.0003392193271 0.0005851701062 0.0006274201144 5.226923831e-05
149 4 74.36502962 -46.44349608 -46.442315 0.0002952704157 0.0009310965085 0.002424436842 0.0003920457138
150 4 74.11860796 -46.43739757 -46.436613 0.0001961425426 0.0005005987575 0.0005321240457 3.638457697e-05
151 4 73.86741001 -46.42888891 -46.430825 0.0004840217708 0.0008314340745 0.001399987143 0.0001492924539
152 4 73.94132612 -46.43138244 -46.43312 0.0004343904872 0.0004971894271 0.0007272771136 6.16242895e-05
153 4 73.9811119 -46.43319833 -46.434347 0.0002871686287 0.0007640297344 0.001284451634 0.0001467135239
154 4 73.82698041 -46.42754585 -46.430573 0.0007567872236 0.0007803200144 0.001315746176 0.0001304502836
155 4 74.70690467 -46.45123289 -46.445665 0.001391971583 0.000912821784 0.00180789159 0.0002496717464
156 4 74.08446722 -46.43563009 -46.435898 6.697700072e-05 0.0007591992871 0.001869300939 0.0002563050641
157 4 74.25274774 -46.44120364 -46.442107 0.0002258396892 0.0005574046688 0.0006020930161 2.324942586e-05
158 4 74.05043726 -46.43500981 -46.434432 0.0001444514979 0.0008611253568 0.001092982159 9.017583814e-05
159 4 74.16653794 -46.43863993 -46.436308 0.0005829826136 0.001060553102 0.001839150891 0.0002291231919
160 4 73.62293094 -46.4201114 -46.423938 0.0009566503804 0.0008574602209 0.001463463016 0.0001901165523
161 4 73.74948122 -46.42480038 -46.428115 0.000828655915 0.0006006578196 0.0008584497656 8.29494047e-05
162 4 73.70731572 -46.42326086 -46.4269 0.0009097854502 0.001062000657 0.001845719914 0.0002324573348
163 4 73.59054722 -46.41944303 -46.421142 0.0004247414002 0.001000176849 0.001309150106 7.649565949e-05
164 4 73.85798892 -46.42896597 -46.432233 0.0008167580325 0.0007130466962 0.0007253109678 2.540277099e-05
165 4 73.86179419 -46.42889661 -46.429408 0.0001278480304 0.0007720172797 0.001068327665 8.148433799e-05
166 4 74.58468636 -46.44869941 -46.445145 0.0008886032859 0.0008714532703 0.001776038288 0.0002327604096
167 4 74.02247797 -46.43395689 -46.435868 0.0004777768694 0.001074996639 0.002376074704 0.0003714110678
168 4 74.20501804 -46.43992891 -46.439663 6.647739254e-05 0.0004913987671 0.001119403413 0.0001129857949
169 4 73.72492498 -46.42387556 -46.428287 0.001102860657 0.001111098987 0.001277000392 4.767829959e-05
170 4 73.62492908 -46.42004351 -46.424584 0.001135123073 0.000608718964 0.0008032957114 4.863049491e-05
171 4 73.28647 -46.40612994 -46.413045 0.001728765173 0.0009572635281 0.001248322074 6.340476344e-05
172 4 74.01119894 -46.43403469 -46.436994 0.0007398269992 0.0008671865748 0.001331939188 0.0001655986986
173 4 74.45838911 -46.44613455 -46.443604 0.0006326364178 0.0007683325186 0.001177046303 0.0001142676877
174 4 74.29439096 -46.4416974 -46.439718 0.0004948490634 7.174265391e-07 0 1.957546294e-07
175 4 74.12581885 -46.43747158 -46.435527 0.0004861456013 0.0009333261572 0.0009338393866 5.564268288e-05
176 4 73.97170625 -46.43318851 -46.434787 0.0003996230226 0.0009611028129 0.00117329195 5.165922942e-05
177 4 74.0799757 -46.43607227 -46.434929 0.0002858162713 0.001070160447 0.001349491756 7.398404571e-05
178 4 73.74433679 -46.42452921 -46.426499 0.0004924477205 0.0009908563993 0.001248937949 7.276928778e-05
179 4 74.14770713 -46.43765471 -46.437025 0.0001574280619 0.0006985490055 0.000938418883 7.194411581e-05
180 4 73.80957625 -46.42673373 -46.428937 0.0005508186891 0.0009773694294 0.001286352984 8.97083467e-05
181 4 74.32407369 -46.44269641 -46.442516 4.5102579e-05 0.0005588761384 0.00094855469 0.0001328512315
182 4 73.84764949 -46.42848088 -46.428736 6.377880708e-05 0.0008336842908 0.001424321593 0.0001503865699
183 4 73.97111028 -46.43238789 -46.433359 0.0002427772064 0.0009694254484 0.001276381604 8.465629047e-05
184 4 74.25298337 -46.44104808 -46.438799 0.0005622709739 0.0007056135708 0.0008186940821 3.512764015e-05
185 4 74.36513571 -46.44345832 -46.441993 0.0003663295202 0.0007496778583 0.001887735151 0.0002557772734
186 4 74.14572274 -46.43778408 -46.439033 0.0003122307984 0.0006954978966 0.000821568013 5.01831345e-05
187 4 74.11964094 -46.43682714 -46.436967 3.496546203e-05 0.0009059931417 0.001482323514 0.0001696649932
188 4 73.76706483 -46.42541677 -46.427245 0.0004570563568 0.0009334393986 0.001293885621 9.590075509e-05
189 4 74.21830016 -46.43974418 -46.438046 0.0004245453121 0.001057167839 0.001627288542 0.0001558520077
190 4 73.51075683 -46.4156415 -46.420083 0.001110373978 0.001244007116 0.002395244873 0.00034823763
191 4 74.62704502 -46.44967068 -46.445247 0.001105920867 0.0007554821414 0.001219330964 0.0001118281973
192 4 74.54172989 -46.44796221 -46.446044 0.0004795523642 0.0007272499601 0.001305329077 0.0001300944459
193 4 74.05152275 -46.43538578 -46.434472 0.0002284439507 0.0007516206255 0.0008323340675 6.16354478e-05
194 4 74.415732 -46.4451924 -46.44458 0.0001530995152 0.0005453483715 0.0009744208536 7.801765207e-05
195 4 74.3298536 -46.44261807 -46.441776 0.0002105168862 0.0009303424865 0.001339231869 0.0001224604469
196 4 74.14951222 -46.43767219 -46.436389 0.0003207973135 0.001073742923 0.001786741168 0.0001836530955
197 4 74.58621137 -46.44886332 -46.446416 0.0006118291188 0.000539216868 0.0006588778339 5.733030195e-05
198 4 74.93791818 -46.4553124 -46.449806 0.001376600758 0.000993833802 0.002135055034 0.0003001159572
199 4 73.6789527 -46.42237113 -46.427189 0.001204468343 0.0008557723942 0.001050788276 5.144154624e-05
200 4 73.72666848 -46.42396926 -46.427857 0.0009719347238 0.0008509822146 0.001487666629 0.0001631640612
201 4 74.38554824 -46.44443534 -46.44004 0.001098835556 0.0005506604143 0.000757202747 5.023582159e-05
202 4 74.09024992 -46.43658234 -46.437214 0.0001579154595 0.0007579523125 0.001505586265 0.0001696548607
203 4 73.60013606 -46.41926939 -46.422628 0.0008396520565 0.0007906960069 0.001601713458 0.0002486017186
204 4 74.47827164 -46.44620312 -46.443535 0.0006670288503 0.001038035933 0.001590304373 0.0001534552128
205 4 74.22558703 -46.43985215 -46.439922 1.746293556e-05 0.0009366011662 0.001530493385 0.0001392156328
206 4 74.15291432 -46.43791295 -46.437675 5.948723777e-05 0.00120593978 0.002440246094 0.0003807637292
207 4 74.50981896 -46.4472593 -46.445558 0.000425326098 0.0007151708815 0.00113392416 0.000110926128
208 4 74.19814905 -46.43963928 -46.439106 0.0001333190449 0.001060221204 0.001830731002 0.0002261342402
209 4 74.51720313 -46.44717428 -46.443073 0.001025321243 0.0004864979524 0.0005766870902 2.649856483e-05
210 4 74.29924604 -46.44212608 -46.4397 0.0006065195947 0.0007431032667 0.001204174406 0.0001052956692
211 4 74.09425795 -46.43641293 -46.436374 9.731942171e-06 0.0008064192 0.001461656594 0.0002109381646
212 4 73.73717548 -46.4244211 -46.426557 0.0005339747042 0.0007876252225 0.001359624213 0.0001150772834
213 4 73.99983876 -46.43299349 -46.434009 0.0002538770585 0.0009202380457 0.001391131194 0.0001428509303
214 4 74.07916779 -46.43553838 -46.436262 0.0001809045988 0.00118187638 0.002503347159 0.0003102016347
215 4 73.94744484 -46.43215124 -46.434505 0.000588441051 0.0009156397335 0.001041637173 3.636515681e-05
216 4 74.2021224 -46.43937206 -46.438768 0.0001510156051 0.0008932395654 0.001098285027 7.635401362e-05
217 4 74.20389194 -46.43949396 -46.440254 0.0001900097138 0.0005024593802 0.0006069892915 5.592088864e-05
218 4 73.66782167 -46.42229787 -46.42286 0.0001405318415 0.0005152726314 0.0007365242698 7.33978531e-05
219 4 73.46349993 -46.41360551 -46.418078 0.001118123388 0.001132433091 0.002028412187 0.000232435598
220 4 74.30307454 -46.44200406 -46.440513 0.0003727657483 0.0007453124106 0.001158189967 0.0001270673971
221 4 73.21819832 -46.40306559 -46.409824 0.001689603747 0.0008129832205 0.001759573812 0.0002263779134
222 4 74.35772636 -46.44356288 -46.440329 0.0008084703191 0.0005476676763 0.0009534044263 9.92864519e-05
223 4 74.17615527 -46.43837738 -46.43773 0.0001618444378 0.0007021754874 0.000926180328 7.195004284e-05
224 4 73.43860935 -46.4128221 -46.416525 0.0009257241101 0.0006236120326 0.0007573664899 4.936853351e-05
225 4 74.31356506 -46.44240466 -46.440293 0.000527914935 0.0007419253152 0.0007725386722 1.336277e-05
226 4 74.25452523 -46.44123444 -46.43839 0.0007111088236 0.0005560993574 0.0005612022808 9.046659076e-06
227 4 74.27331932 -46.44216076 -46.438916 0.0008111897329 0.0007444767412 0.001650878554 0.0002044035839
128 4 74.14589882 -46.43773689 -46.437936 4.977777772e-05 0.0007580062919 0.001265949446 0.0001549130008
129 4 74.26852111 -46.44163804 -46.438504 0.0007835093466 0.0007928704138 0.001492549497 0.0001864512424
130 4 74.05957274 -46.4350456 -46.436378 0.0003331000629 0.000501045122 0.000810592376 0.0001083761555
131 4 74.30647158 -46.44214696 -46.441551 0.0001489890131 0.0009248081405 0.001283675193 0.0001072340337
132 4 73.40902276 -46.41147984 -46.416957 0.001369290658 0.0008053997592 0.001186145859 0.00010805291
133 4 74.1804881 -46.43910949 -46.440495 0.000346377798 0.0008002026566 0.001212440514 9.528590247e-05
134 4 74.17596744 -46.43848913 -46.437972 0.0001292833847 0.001183921884 0.002358226452 0.0002970860066
135 4 74.73528136 -46.45170361 -46.44586 0.001460903385 0.001133139777 0.002033949852 0.0002537828814
136 4 74.0787509 -46.43566767 -46.435744 1.908313726e-05 0.0008616113593 0.001690849491 0.0002669026715
137 4 74.24609528 -46.44080156 -46.438209 0.0006481400478 0.0007503717979 0.001160049999 9.912563445e-05
138 4 73.73005434 -46.42419116 -46.42629 0.0005247105691 0.0004976402642 0.0005297018029 1.258359709e-05
139 4 74.33993289 -46.44322432 -46.443301 1.917100383e-05 0.0009242720079 0.001818421568 0.0002230028975
140 4 74.20715045 -46.43973495 -46.439002 0.0001832366414 0.001024144871 0.001416973535 0.0001023494159
141 4 73.89686848 -46.43019548 -46.432438 0.0005606290131 0.0009638851957 0.001010469198 5.947391544e-05
142 4 73.27773838 -46.40573759 -46.412654 0.001729102505 0.001208977045 0.001801959766 0.0001722771521
143 4 74.40027968 -46.44461578 -46.443231 0.0003461945846 0.0007381685163 0.001691590967 0.000203952546
144 4 73.86123747 -46.42927593 -46.431513 0.0005592673238 0.001235982264 0.001680544852 0.0001101441056
145 4 73.96908649 -46.43260512 -46.435608 0.00075071992 0.0007552771558 0.0009593039143 4.8360346e-05
146 4 74.18717232 -46.43958279 -46.437689 0.0004734476282 0.0007940403628 0.001217708504 0.0001255353934
147 4 73.76897316 -46.42538037 -46.428447 0.0007666567748 0.0009193516438 0.002060081552 0.0002986539508
148 4 73.9161373 -46.43089812 -46.432255 0.0003392206286 0.0005851688476 0.0006274201144 5.2269038e-05
149 4 74.36502962 -46.44349609 -46.442315 0.0002952728767 0.0009310955601 0.002424436842 0.0003920459666
150 4 74.11860796 -46.43739757 -46.436613 0.000196142977 0.000500599652 0.0005321240457 3.638443329e-05
151 4 73.86741001 -46.42888891 -46.430825 0.0004840235444 0.0008314322693 0.001399987143 0.0001492928826
152 4 73.94132612 -46.43138243 -46.43312 0.0004343916658 0.000497190216 0.0007272771136 6.162416996e-05
153 4 73.9811119 -46.43319832 -46.434347 0.0002871694162 0.0007640293471 0.001284451634 0.0001467135868
154 4 73.82698041 -46.42754584 -46.430573 0.0007567894836 0.0007803196447 0.001315746176 0.000130450336
155 4 74.70690467 -46.45123291 -46.445665 0.001391976789 0.0009128197805 0.00180789159 0.0002496723251
156 4 74.08446722 -46.43563009 -46.435898 6.697704207e-05 0.0007591988888 0.001869300939 0.0002563052659
157 4 74.25274774 -46.44120365 -46.442107 0.0002258380937 0.0005574034148 0.0006020930161 2.324961995e-05
158 4 74.05043726 -46.4350098 -46.434432 0.000144451142 0.0008611268258 0.001092982159 9.017555815e-05
159 4 74.16653794 -46.43863993 -46.436308 0.0005829833566 0.00106055254 0.001839150891 0.000229123465
160 4 73.62293094 -46.42011138 -46.423938 0.0009566541712 0.0008574583854 0.001463463016 0.0001901167955
161 4 73.74948122 -46.42480037 -46.428115 0.000828658679 0.0006006566124 0.0008584497656 8.294960318e-05
162 4 73.70731572 -46.42326085 -46.4269 0.0009097885843 0.001062001258 0.001845719914 0.0002324573925
163 4 73.59054722 -46.41944302 -46.421142 0.0004247454009 0.001000175845 0.001309150106 7.649587937e-05
164 4 73.85798892 -46.42896596 -46.432233 0.0008167597726 0.0007130478918 0.0007253109678 2.54027938e-05
165 4 73.86179419 -46.4288966 -46.429408 0.0001278497417 0.0007720169229 0.001068327665 8.148439828e-05
166 4 74.58468636 -46.44869943 -46.445145 0.0008886073529 0.0008714532974 0.001776038288 0.0002327605041
167 4 74.02247797 -46.43395689 -46.435868 0.0004777774607 0.001074996059 0.002376074704 0.0003714114709
168 4 74.20501804 -46.43992891 -46.439663 6.647857783e-05 0.0004913996071 0.001119403413 0.0001129856447
169 4 73.72492498 -46.42387555 -46.428287 0.001102863629 0.001111098449 0.001277000392 4.767855511e-05
170 4 73.62492908 -46.42004349 -46.424584 0.00113512691 0.0006087177129 0.0008032957114 4.863069832e-05
171 4 73.28647 -46.40612991 -46.413045 0.001728771812 0.0009572637029 0.001248322074 6.340444936e-05
172 4 74.01119894 -46.43403469 -46.436994 0.0007398275139 0.0008671879206 0.001331939188 0.0001655984492
173 4 74.45838911 -46.44613456 -46.443604 0.0006326396057 0.0007683307853 0.001177046303 0.0001142678741
174 4 74.29439096 -46.4416974 -46.439718 0.0004948508087 7.174250053e-07 0 1.957542072e-07
175 4 74.12581885 -46.43747158 -46.435527 0.0004861461336 0.0009333249455 0.0009338393866 5.564266447e-05
176 4 73.97170625 -46.43318851 -46.434787 0.000399623642 0.000961101783 0.00117329195 5.165964937e-05
177 4 74.0799757 -46.43607227 -46.434929 0.0002858164295 0.001070159815 0.001349491756 7.398431987e-05
178 4 73.74433679 -46.4245292 -46.426499 0.0004924505278 0.0009908554146 0.001248937949 7.276971014e-05
179 4 74.14770713 -46.43765471 -46.437025 0.0001574286401 0.0006985501267 0.000938418883 7.194396974e-05
180 4 73.80957625 -46.42673372 -46.428937 0.0005508209822 0.0009773683565 0.001286352984 8.970876067e-05
181 4 74.32407369 -46.44269642 -46.442516 4.510464404e-05 0.0005588750063 0.00094855469 0.0001328514234
182 4 73.84764949 -46.42848088 -46.428736 6.378070081e-05 0.0008336824804 0.001424321593 0.0001503869995
183 4 73.97111028 -46.43238789 -46.433359 0.0002427779743 0.0009694245039 0.001276381604 8.465668861e-05
184 4 74.25298337 -46.44104809 -46.438799 0.0005622725854 0.0007056146897 0.0008186940821 3.51276601e-05
185 4 74.36513571 -46.44345833 -46.441993 0.000366331938 0.0007496775711 0.001887735151 0.0002557773166
186 4 74.14572274 -46.43778408 -46.439033 0.0003122302764 0.0006954989644 0.000821568013 5.018300353e-05
187 4 74.11964094 -46.43682714 -46.436967 3.496532598e-05 0.0009059932494 0.001482323514 0.0001696650679
188 4 73.76706483 -46.42541676 -46.427245 0.0004570589281 0.0009334396333 0.001293885621 9.590044259e-05
189 4 74.21830016 -46.43974419 -46.438046 0.0004245463831 0.001057167246 0.001627288542 0.0001558522948
190 4 73.51075683 -46.41564148 -46.420083 0.001110378787 0.001244007139 0.002395244873 0.000348238222
191 4 74.62704502 -46.4496707 -46.445247 0.001105925387 0.0007554805093 0.001219330964 0.0001118285779
192 4 74.54172989 -46.44796223 -46.446044 0.0004795562678 0.0007272495607 0.001305329077 0.0001300945224
193 4 74.05152275 -46.43538578 -46.434472 0.0002284439223 0.0007516201482 0.0008323340675 6.163582106e-05
194 4 74.415732 -46.44519241 -46.44458 0.0001531024275 0.0005453471413 0.0009744208536 7.801785777e-05
195 4 74.3298536 -46.44261808 -46.441776 0.0002105187947 0.0009303414838 0.001339231869 0.0001224608365
196 4 74.14951222 -46.43767219 -46.436389 0.0003207979254 0.001073742431 0.001786741168 0.0001836533518
197 4 74.58621137 -46.44886333 -46.446416 0.0006118332796 0.0005392157373 0.0006588778339 5.733048122e-05
198 4 74.93791818 -46.45531243 -46.449806 0.001376607767 0.0009938332075 0.002135055034 0.0003001163339
199 4 73.6789527 -46.42237111 -46.427189 0.001204471625 0.0008557706472 0.001050788276 5.144194784e-05
200 4 73.72666848 -46.42396925 -46.427857 0.0009719377199 0.0008509804746 0.001487666629 0.0001631644785
201 4 74.38554824 -46.44443535 -46.44004 0.001098838369 0.0005506592059 0.000757202747 5.023604045e-05
202 4 74.09024992 -46.43658234 -46.437214 0.0001579151675 0.0007579519019 0.001505586265 0.0001696550305
203 4 73.60013606 -46.41926938 -46.422628 0.0008396561265 0.0007906956284 0.001601713458 0.0002486017678
204 4 74.47827164 -46.44620313 -46.443535 0.0006670323462 0.001038035307 0.001590304373 0.0001534556262
205 4 74.22558703 -46.43985215 -46.439922 1.746193486e-05 0.0009366001229 0.001530493385 0.0001392158714
206 4 74.15291432 -46.43791295 -46.437675 5.948778087e-05 0.001205938705 0.002440246094 0.0003807643418
207 4 74.50981896 -46.44725932 -46.445558 0.0004253297194 0.0007151703383 0.00113392416 0.0001109262358
208 4 74.19814905 -46.43963928 -46.439106 0.0001333200909 0.001060220661 0.001830731002 0.0002261345173
209 4 74.51720313 -46.4471743 -46.443073 0.001025324977 0.0004864986306 0.0005766870902 2.649843773e-05
210 4 74.29924604 -46.44212609 -46.4397 0.0006065214392 0.0007431028884 0.001204174406 0.0001052957467
211 4 74.09425795 -46.43641293 -46.436374 9.732172606e-06 0.0008064174002 0.001461656594 0.0002109385778
212 4 73.73717548 -46.42442109 -46.426557 0.0005339776769 0.0007876249052 0.001359624213 0.0001150774771
213 4 73.99983876 -46.43299349 -46.434009 0.0002538777661 0.0009202382455 0.001391131194 0.0001428509871
214 4 74.07916779 -46.43553838 -46.436262 0.0001809047926 0.0011818762 0.002503347159 0.0003102017009
215 4 73.94744484 -46.43215123 -46.434505 0.0005884419203 0.0009156398008 0.001041637173 3.636510316e-05
216 4 74.2021224 -46.43937207 -46.438768 0.0001510167595 0.0008932396391 0.001098285027 7.635410844e-05
217 4 74.20389194 -46.43949397 -46.440254 0.0001900086608 0.000502460176 0.0006069892915 5.592074903e-05
218 4 73.66782167 -46.42229786 -46.42286 0.0001405350172 0.0005152736108 0.0007365242698 7.339770756e-05
219 4 73.46349993 -46.41360549 -46.418078 0.001118128508 0.001132432533 0.002028412187 0.0002324355004
220 4 74.30307454 -46.44200407 -46.440513 0.0003727676166 0.0007453119816 0.001158189967 0.0001270674696
221 4 73.21819832 -46.40306556 -46.409824 0.001689610925 0.0008129827577 0.001759573812 0.0002263779933
222 4 74.35772636 -46.44356289 -46.440329 0.0008084725995 0.000547666406 0.0009534044263 9.928667432e-05
223 4 74.17615527 -46.43837738 -46.43773 0.0001618451623 0.0007021766311 0.000926180328 7.194991709e-05
224 4 73.43860935 -46.41282208 -46.416525 0.0009257293928 0.0006236107992 0.0007573664899 4.936874917e-05
225 4 74.31356506 -46.44240467 -46.440293 0.0005279168378 0.0007419249252 0.0007725386722 1.336311633e-05
226 4 74.25452523 -46.44123444 -46.43839 0.0007111104861 0.0005560980711 0.0005612022808 9.046877182e-06
227 4 74.27331932 -46.44216077 -46.438916 0.0008111916537 0.0007444763728 0.001650878554 0.0002044036492
# GSF_110.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
228 24 828.0362386 -278.8565429 -279.068761 0.008842419523 1.256462937 1.756353161 0.051477507
229 24 828.0362386 -279.8906758 -279.784296 0.004432490554 0.9837362604 0.9057668891 0.04530614868
230 24 828.0362386 -279.9855692 -279.901657 0.003496340045 0.5437503433 0.001565946359 0.02630578972
231 24 828.0362386 -279.6358344 -279.584238 0.002149848085 1.366344365 1.035572248 0.05866356809
232 24 828.0362386 -279.890679 -279.784283 0.00443316818 0.9837290842 0.9056396189 0.04530262093
233 24 828.0362386 -279.2626859 -279.302158 0.00164466906 1.823227496 1.771965137 0.06079518696
234 24 828.0362386 -279.6168585 -279.55564 0.002550771678 1.594742608 1.405626506 0.05621457826
235 24 828.0362386 -279.024762 -279.246939 0.009257376041 1.056637483 0.4813964151 0.05829914373
236 24 828.0362386 -279.2626909 -279.302157 0.001644419804 1.823235211 1.771953347 0.06079386829
237 24 828.0362386 -279.02461 -279.246935 0.009263540157 1.057239554 0.4809484798 0.05825119217
238 24 828.0362386 -279.985518 -279.896025 0.0037288749 0.5432874641 0.01060549839 0.0262491982
239 24 828.0362386 -279.6357454 -279.584237 0.002146182283 1.367395655 1.035836121 0.05866152337
240 24 828.0362386 -278.9679742 -279.124427 0.006518866753 1.537790203 1.809545887 0.06158995911
241 24 828.0362386 -279.3090025 -279.379366 0.002931810503 1.425871851 0.8982692706 0.0597426964
242 24 828.0362386 -279.3089672 -279.37937 0.002933449942 1.42610803 0.898081355 0.05974840266
243 24 828.0362386 -278.9679713 -279.124427 0.006518987217 1.537779408 1.809523374 0.0615901037
244 24 828.0362386 -279.9855692 -279.901657 0.003496340045 0.5437503444 0.001570374478 0.02630356435
245 24 828.0362386 -279.8927781 -279.79264 0.004172421011 0.9365657748 0.8392614852 0.04790548616
246 24 828.0362386 -279.985518 -279.896025 0.003728874899 0.543287463 0.01060243293 0.0262493683
247 24 828.0362386 -278.9127231 -279.206496 0.01224053829 0.6560191316 0.005326518563 0.04091282266
248 24 828.0362386 -279.6168637 -279.55564 0.002550987356 1.594742102 1.4056319 0.05621528543
249 24 828.0362386 -279.892787 -279.79264 0.004172793182 0.9364911788 0.8392625708 0.04790468457
228 24 828.0362386 -278.8565431 -279.068761 0.00884241053 1.256467488 1.756353161 0.05147748088
229 24 828.0362386 -279.8906755 -279.784296 0.004432481137 0.9837376748 0.9057668891 0.04530617567
230 24 828.0362386 -279.9855689 -279.901657 0.003496329946 0.5437520363 0.001565946359 0.02630584952
231 24 828.0362386 -279.6358341 -279.584238 0.002149836895 1.366345904 1.035572248 0.05866362655
232 24 828.0362386 -279.8906788 -279.784283 0.004433158764 0.9837304986 0.9056396189 0.04530264792
233 24 828.0362386 -279.2626857 -279.302158 0.001644679061 1.823229154 1.771965137 0.06079521213
234 24 828.0362386 -279.6168583 -279.55564 0.002550761293 1.59474416 1.405626506 0.05621460711
235 24 828.0362386 -279.0247621 -279.246939 0.009257370765 1.056637844 0.4813964151 0.05829919761
236 24 828.0362386 -279.2626907 -279.302157 0.001644429805 1.823236869 1.771953347 0.06079389345
237 24 828.0362386 -279.0246102 -279.246935 0.009263534933 1.057239919 0.4809484798 0.05825124616
238 24 828.0362386 -279.9855178 -279.896025 0.003728864801 0.5432891464 0.01060549839 0.02624925791
239 24 828.0362386 -279.6357451 -279.584237 0.002146171098 1.367397194 1.035836121 0.05866158171
240 24 828.0362386 -278.9679742 -279.124427 0.006518865028 1.537792854 1.809545887 0.06158995045
241 24 828.0362386 -279.3090023 -279.379366 0.002931819836 1.425872718 0.8982692706 0.05974280483
242 24 828.0362386 -279.308967 -279.37937 0.002933459274 1.426108897 0.898081355 0.05974851115
243 24 828.0362386 -278.9679713 -279.124427 0.006518985491 1.537782059 1.809523374 0.06159009503
244 24 828.0362386 -279.9855689 -279.901657 0.003496329946 0.5437520374 0.001570374478 0.02630362414
245 24 828.0362386 -279.8927779 -279.79264 0.004172411542 0.9365672266 0.8392614852 0.04790551261
246 24 828.0362386 -279.9855178 -279.896025 0.003728864801 0.5432891453 0.01060243293 0.02624942801
247 24 828.0362386 -278.9127235 -279.206496 0.01224052222 0.6560211144 0.005326518563 0.04091291383
248 24 828.0362386 -279.6168634 -279.55564 0.00255097697 1.594743654 1.4056319 0.05621531428
249 24 828.0362386 -279.8927868 -279.79264 0.004172783713 0.9364926305 0.8392625708 0.04790471101
# GSF_112.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
250 30 1075.650827 -344.9649922 -345.175835 0.007028094833 1.824275865 1.057395322 0.06767106212
251 30 1075.650827 -346.6372632 -346.361714 0.009184971937 1.212446362 1.220284939 0.05182279643
252 30 1075.650827 -346.0996792 -345.795524 0.01013850798 2.074559881 2.112860875 0.05606482283
253 30 1075.650827 -344.7280032 -345.164602 0.01455329455 2.055943496 1.765832199 0.0545384664
254 30 1075.650827 -346.8075692 -346.593523 0.007134872899 0.7292863081 0.01148867129 0.05478897035
255 30 1075.650827 -346.6119055 -346.396186 0.007190649998 1.417584921 0.9954683928 0.06448704265
256 30 1075.650827 -344.927849 -345.319406 0.01305189861 2.486024431 1.772040852 0.06040783095
257 30 1075.650827 -345.4538269 -345.594794 0.004698901737 2.654358849 1.516014157 0.07318786038
258 30 1075.650827 -346.0897537 -345.98566 0.003469789702 2.222053757 1.406252265 0.07377712375
259 30 1075.650827 -345.5371738 -345.383994 0.005105992678 1.942796632 0.963574308 0.06626680321
260 30 1075.650827 -346.8076141 -346.582564 0.007501671616 0.7294986697 0.0126740587 0.05485197859
261 30 1075.650827 -345.3513955 -345.452139 0.003358116903 3.516499349 2.787719406 0.0833137189
262 30 1075.650827 -346.8075718 -346.593523 0.007134958623 0.7292691472 0.01148834 0.05478819492
263 30 1075.650827 -345.4031277 -345.281949 0.004039288726 2.350925681 1.873142686 0.06504602591
264 30 1075.650827 -346.0710518 -345.928661 0.004746361529 2.713948369 2.100874472 0.07900703123
265 30 1075.650827 -344.7648314 -345.111657 0.0115608538 3.420286553 3.358068319 0.07195512437
266 30 1075.650827 -346.6271156 -346.367123 0.008666420776 1.309082813 1.335797131 0.05280237502
267 30 1075.650827 -346.8076229 -346.582565 0.00750192922 0.7290652079 0.01254743735 0.05484163416
268 30 1075.650827 -344.5588847 -344.91356 0.01182251118 2.831189284 3.441834403 0.07248927965
269 30 1075.650827 -346.1710412 -345.836703 0.01114460652 1.76643717 1.608769148 0.05038562968
270 30 1075.650827 -344.80319 -344.984307 0.006037234982 2.373757292 2.542628782 0.06899631184
271 30 1075.650827 -346.619143 -346.393931 0.00750706759 1.537444349 1.211680725 0.06667728989
250 30 1075.650827 -344.9649936 -345.175835 0.007028045401 1.824277067 1.057395322 0.06767088379
251 30 1075.650827 -346.6372643 -346.361714 0.009185008801 1.212447793 1.220284939 0.0518228667
252 30 1075.650827 -346.0996806 -345.795524 0.01013855364 2.074559425 2.112860875 0.05606480427
253 30 1075.650827 -344.7280048 -345.164602 0.01455323871 2.055944476 1.765832199 0.05453853965
254 30 1075.650827 -346.8075702 -346.593523 0.007134907583 0.7292885354 0.01148867129 0.05478892337
255 30 1075.650827 -346.6119066 -346.396186 0.007190686192 1.417586653 0.9954683928 0.06448697912
256 30 1075.650827 -344.9278501 -345.319406 0.01305186302 2.486024454 1.772040852 0.0604078804
257 30 1075.650827 -345.4538275 -345.594794 0.004698882831 2.654360962 1.516014157 0.07318802801
258 30 1075.650827 -346.0897545 -345.98566 0.00346981812 2.222056549 1.406252265 0.07377719261
259 30 1075.650827 -345.5371748 -345.383994 0.005106027107 1.94279858 0.963574308 0.06626681948
260 30 1075.650827 -346.8076152 -346.582564 0.007501706217 0.7295008894 0.0126740587 0.05485193126
261 30 1075.650827 -345.3513957 -345.452139 0.003358110458 3.516505089 2.787719406 0.0833138344
262 30 1075.650827 -346.8075728 -346.593523 0.007134993308 0.7292713747 0.01148834 0.05478814795
263 30 1075.650827 -345.4031291 -345.281949 0.004039338109 2.350924882 1.873142686 0.06504604962
264 30 1075.650827 -346.0710525 -345.928661 0.004746382876 2.71395353 2.100874472 0.07900720207
265 30 1075.650827 -344.7648319 -345.111657 0.01156083551 3.420290291 3.358068319 0.07195517952
266 30 1075.650827 -346.6271168 -346.367123 0.008666459828 1.309083618 1.335797131 0.05280244013
267 30 1075.650827 -346.8076239 -346.582565 0.007501963803 0.7290674311 0.01254743735 0.0548415869
268 30 1075.650827 -344.558886 -344.91356 0.01182246624 2.831191281 3.441834403 0.07248927525
269 30 1075.650827 -346.1710422 -345.836703 0.01114463898 1.766439383 1.608769148 0.05038575671
270 30 1075.650827 -344.8031917 -344.984307 0.006037177924 2.373757277 2.542628782 0.0689962124
271 30 1075.650827 -346.619144 -346.393931 0.007507101293 1.53744705 1.211680725 0.0666772296
# Liquid.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
272 100 2002.996789 -1105.231792 -1105.601723 0.003699309182 31.93365739 31.39853886 0.3605920438
273 100 2002.996789 -1100.0483 -1099.673012 0.003752881812 34.04378497 32.03167218 0.3801372404
274 100 2002.996789 -1122.950983 -1121.31506 0.01635922878 20.51804501 20.81076453 0.3053008452
272 100 2002.996789 -1105.231809 -1105.601723 0.003699138194 31.93361219 31.39853886 0.3605924612
273 100 2002.996789 -1100.048286 -1099.673012 0.003752740408 34.04382223 32.03167218 0.3801389343
274 100 2002.996789 -1122.950971 -1121.31506 0.01635910776 20.51802979 20.81076453 0.3053007331
# Surface.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
275 24 828.0362197 -279.9855176 -279.911828 0.003070401068 0.5432872547 0.002753093533 0.02662363109
276 48 1756.536679 -553.7206131 -555.359452 0.03414247756 1.327934241 0.003020630398 0.05062757505
277 40 1394.433693 -459.4032557 -459.216162 0.004677342867 5.707257775 5.0461364 0.06575510851
278 40 1394.433693 -460.9407014 -461.144076 0.005084365239 1.226822831 0.005582740008 0.05122547537
279 24 828.0362197 -279.8655607 -279.635146 0.009600610902 1.408375724 1.288799837 0.01913605472
280 30 1075.65076 -346.8075686 -346.592525 0.007168120862 0.7292871829 0.008446203407 0.0545558719
281 30 1075.65076 -346.0293144 -345.744506 0.009493613698 3.606298321 3.124961367 0.0570139916
275 24 828.0362197 -279.9855174 -279.911828 0.00307039097 0.543288937 0.002753093533 0.02662369048
276 48 1756.536679 -553.720609 -555.359452 0.0341425618 1.32792499 0.003020630398 0.05062733253
277 40 1394.433693 -459.4032432 -459.216162 0.004677029808 5.707232519 5.0461364 0.06575417121
278 40 1394.433693 -460.9406827 -461.144076 0.005084831715 1.226813498 0.005582740008 0.05122491857
279 24 828.0362197 -279.8655605 -279.635146 0.009600605095 1.408377316 1.288799837 0.01913613462
280 30 1075.65076 -346.8075697 -346.592525 0.007168155546 0.7292894102 0.008446203407 0.05455582493
281 30 1075.65076 -346.0293205 -345.744506 0.009493817024 3.606285447 3.124961367 0.05701335452
# Volume_A15.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
282 8 300.763 -67.0021096 -66.990732 0.001422200411 2.60703787e-14 0 4.250969508e-15
283 8 97.336 -72.96680402 -72.957807 0.001124627087 3.773524369e-13 0 6.23442999e-14
284 8 140.608 -94.17243588 -94.145745 0.003336359862 1.552250892e-13 0 2.138296916e-14
285 8 148.877 -94.52476758 -94.554682 0.003739302767 1.513273305e-13 0 2.299437315e-14
286 8 103.823 -79.4027843 -79.438363 0.004447338001 3.128019921e-13 0 5.076423719e-14
287 8 287.496 -69.6488013 -69.627817 0.002623037281 2.303580727e-14 0 3.804919931e-15
288 8 226.981 -82.5857428 -82.604907 0.002395525023 1.948385656e-14 0 2.991996515e-15
289 8 64 14.91754962 14.89048 0.003383703009 1.311121193e-12 0 2.189143418e-13
290 8 157.464 -94.29253765 -94.367599 0.009382668586 7.283093784e-14 0 1.265997243e-14
291 8 195.112 -89.21981877 -89.248227 0.003551028811 6.140862651e-14 0 9.766840787e-15
292 8 205.379 -87.19055665 -87.211997 0.002680043619 5.806101694e-14 0 9.12591423e-15
293 8 166.375 -93.58572576 -93.66897 0.01040552996 6.398102027e-14 0 1.079845551e-14
294 8 68.921 -8.066154558 -7.989166 0.009623569715 1.515100764e-12 0 2.355101946e-13
295 8 216 -84.9634516 -84.982834 0.002422799416 2.468117965e-14 0 3.808086309e-15
296 8 175.616 -92.47115379 -92.536373 0.008152400831 6.796024276e-14 0 1.172118881e-14
297 8 74.088 -26.75167825 -26.77612 0.003055218998 1.342705393e-12 0 2.240627737e-13
298 8 250.047 -77.53664746 -77.544107 0.0009324425707 3.40035775e-14 0 5.629263689e-15
299 8 238.328 -80.09858879 -80.114217 0.00195352648 3.721929684e-14 0 5.33754263e-15
300 8 79.507 -42.08958867 -42.143041 0.006681541494 1.01413587e-12 0 1.644620364e-13
301 8 185.193 -90.9987096 -91.040671 0.005245175536 7.139606115e-14 0 1.073386579e-14
302 8 110.592 -84.43239313 -84.499231 0.00835473392 3.29267204e-13 0 5.241784867e-14
303 8 328.509 -61.71305458 -61.825173 0.01401480302 2.758053378e-14 0 4.502714044e-15
304 8 125 -91.17544034 -91.156873 0.002320917614 1.58668545e-13 0 2.62899222e-14
305 8 85.184 -54.66314958 -54.658744 0.0005506975507 9.547738767e-13 0 1.435990893e-13
306 8 274.625 -72.29366775 -72.277255 0.002051593261 2.759011182e-14 0 4.259388108e-15
307 8 262.144 -74.92790079 -74.923334 0.0005708486151 3.022510628e-14 0 4.93256115e-15
308 8 91.125 -64.83470341 -64.798066 0.004579676092 6.045890849e-13 0 9.477550235e-14
309 8 132.651 -93.09990098 -93.048342 0.006444873045 1.661474782e-13 0 2.626190151e-14
310 8 314.432 -64.3570834 -64.38702 0.003742074757 2.6627152e-14 0 4.932152342e-15
311 8 117.649 -88.30639474 -88.352871 0.005809532749 3.718246964e-13 0 6.108657724e-14
282 8 300.763 -67.00211072 -66.990732 0.001422340526 2.651635999e-14 0 4.496299415e-15
283 8 97.336 -72.96680397 -72.957807 0.00112462123 4.138151186e-13 0 6.631061533e-14
284 8 140.608 -94.17243561 -94.145745 0.003336326154 1.673692449e-13 0 2.404187472e-14
285 8 148.877 -94.5247675 -94.554682 0.003739312923 1.177295187e-13 0 1.964763325e-14
286 8 103.823 -79.40278453 -79.438363 0.004447308954 3.694816886e-13 0 6.439453841e-14
287 8 287.496 -69.64880149 -69.627817 0.002623060816 2.224194614e-14 0 3.564010735e-15
288 8 226.981 -82.58574187 -82.604907 0.002395640945 2.457311331e-14 0 3.26903369e-15
289 8 64 14.91754976 14.89048 0.003383720235 1.617184826e-12 0 2.671720383e-13
290 8 157.464 -94.2925378 -94.367599 0.009382649855 6.644959591e-14 0 1.107198171e-14
291 8 195.112 -89.21981891 -89.248227 0.003551011564 4.812363832e-14 0 7.213657893e-15
292 8 205.379 -87.19055643 -87.211997 0.002680071448 5.441242046e-14 0 9.816384952e-15
293 8 166.375 -93.58572611 -93.66897 0.01040548664 6.884833673e-14 0 1.177896312e-14
294 8 68.921 -8.066154085 -7.989166 0.009623510566 1.649852842e-12 0 2.642371793e-13
295 8 216 -84.963451 -84.982834 0.002422875025 2.491328031e-14 0 3.749941648e-15
296 8 175.616 -92.47115424 -92.536373 0.008152344748 7.201502359e-14 0 1.123793958e-14
297 8 74.088 -26.75167854 -26.77612 0.003055181999 1.193084873e-12 0 1.92865237e-13
298 8 250.047 -77.53664632 -77.544107 0.0009325849132 2.307666185e-14 0 3.635711645e-15
299 8 238.328 -80.09858767 -80.114217 0.001953666808 4.462620321e-14 0 6.223366295e-15
300 8 79.507 -42.08958939 -42.143041 0.006681451198 9.257392066e-13 0 1.61989823e-13
301 8 185.193 -90.99870998 -91.040671 0.005245127037 5.425124507e-14 0 8.470682662e-15
302 8 110.592 -84.43239362 -84.499231 0.008354672769 2.922476594e-13 0 4.951739741e-14
303 8 328.509 -61.71305818 -61.825173 0.01401435208 1.975787159e-14 0 2.944967659e-15
304 8 125 -91.17544063 -91.156873 0.002320953406 1.373431141e-13 0 2.120726391e-14
305 8 85.184 -54.66314991 -54.658744 0.0005507393391 6.498019988e-13 0 1.03139951e-13
306 8 274.625 -72.29366725 -72.277255 0.002051530782 2.719756268e-14 0 4.215441288e-15
307 8 262.144 -74.92789985 -74.923334 0.0005707312568 2.09774975e-14 0 3.177043718e-15
308 8 91.125 -64.83470334 -64.798066 0.00457966782 5.72434976e-13 0 8.216595723e-14
309 8 132.651 -93.09990078 -93.048342 0.006444846928 2.069825319e-13 0 3.182927816e-14
310 8 314.432 -64.35708568 -64.38702 0.003741790297 3.663453064e-14 0 5.697289325e-15
311 8 117.649 -88.30639533 -88.352871 0.005809459346 2.91835844e-13 0 4.497446889e-14
# Volume_BCC.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
312 2 74.088 -16.68511706 -16.763625 0.03925396753 2.808666775e-15 0 8.881784197e-16
313 2 13.824 16.36897492 16.314145 0.0274149625 9.181960839e-13 0 3.079018522e-13
314 2 27 -21.21187321 -21.209071 0.00140110742 6.815283523e-14 0 2.368474948e-14
315 2 21.952 -15.77028649 -15.780524 0.005118757155 1.425491777e-13 0 5.477100255e-14
316 2 24.389 -19.01259468 -19.002205 0.005194838855 8.350379207e-14 0 2.592370762e-14
317 2 29.791 -22.64605006 -22.620568 0.01274102801 7.263540276e-14 0 2.723747154e-14
318 2 15.625 4.054805835 4.096885 0.02103958266 1.238995843e-12 0 3.623767952e-13
319 2 10.648 56.26548696 56.26276 0.001363478864 5.516348171e-12 0 1.716959908e-12
320 2 46.656 -22.58541599 -22.585113 0.0001514940573 4.899493581e-14 0 1.983598471e-14
321 2 50.653 -21.79073835 -21.795501 0.002381327165 1.031970068e-14 0 3.552713679e-15
322 2 12.167 33.08450331 33.110078 0.01278734337 3.323639124e-13 0 8.526512829e-14
323 2 54.872 -20.87706988 -20.885998 0.004464061509 7.064325638e-15 0 2.433238796e-15
324 2 39.304 -23.58125163 -23.601336 0.01004218385 4.143140511e-14 0 1.65793305e-14
325 2 42.875 -23.20441311 -23.207313 0.0014499456 5.172829197e-14 0 1.894780629e-14
326 2 59.319 -19.88594939 -19.898089 0.0060698064 1.073706784e-14 0 4.255854928e-15
327 2 32.768 -23.4251645 -23.405474 0.009845249193 2.610700715e-14 0 8.289665251e-15
328 2 17.576 -4.795746708 -4.781324 0.00721135418 2.930611958e-13 0 1.071735293e-13
329 2 64 -18.8457274 -18.864936 0.009604298412 3.833084184e-15 0 1.258252761e-15
330 2 68.921 -17.77479882 -17.813086 0.01914358791 3.662053439e-15 0 1.184237893e-15
331 2 19.683 -11.16052557 -11.197201 0.01833771644 1.393336531e-13 0 5.358676466e-14
332 2 35.937 -23.68631823 -23.696705 0.005193382818 2.461392239e-14 0 9.473903143e-15
312 2 74.088 -16.68511674 -16.763625 0.03925413136 2.264419547e-15 0 7.401486831e-16
313 2 13.824 16.36897512 16.314145 0.02741506046 1.276566703e-12 0 4.09746311e-13
314 2 27 -21.21187309 -21.209071 0.001401043567 5.024293136e-14 0 1.657932212e-14
315 2 21.952 -15.77028666 -15.780524 0.005118671171 3.088780127e-13 0 1.196080272e-13
316 2 24.389 -19.01259482 -19.002205 0.005194909925 5.762720599e-14 0 1.881828027e-14
317 2 29.791 -22.64604984 -22.620568 0.01274091911 3.657742603e-14 0 1.065814104e-14
318 2 15.625 4.054805397 4.096885 0.02103980173 1.189273226e-12 0 3.611925573e-13
319 2 10.648 56.26548696 56.26276 0.001363481826 4.717097082e-12 0 1.573778145e-12
320 2 46.656 -22.58541626 -22.585113 0.0001516282628 5.19489476e-14 0 2.10202226e-14
321 2 50.653 -21.79073862 -21.795501 0.002381191888 5.958081968e-15 0 2.072416313e-15
322 2 12.167 33.08450329 33.110078 0.01278735434 8.874675925e-14 0 3.3158661e-14
323 2 54.872 -20.87707002 -20.885998 0.004463988191 1.053235412e-14 0 3.950543596e-15
324 2 39.304 -23.5812516 -23.601336 0.01004220206 4.49386684e-14 0 1.421085472e-14
325 2 42.875 -23.20441324 -23.207313 0.001449878075 1.421085472e-14 0 4.736951572e-15
326 2 59.319 -19.88594934 -19.898089 0.006069829158 3.244411908e-14 0 1.261028319e-14
327 2 32.768 -23.42516447 -23.405474 0.009845236296 5.364480014e-14 0 2.131628207e-14
328 2 17.576 -4.79574662 -4.781324 0.007211310011 1.842793647e-13 0 6.217248938e-14
329 2 64 -18.84572718 -18.864936 0.009604411802 2.962444526e-15 0 9.62193288e-16
330 2 68.921 -17.77479849 -17.813086 0.01914375282 2.264419547e-15 0 7.401486831e-16
331 2 19.683 -11.16052541 -11.197201 0.0183377973 1.664570528e-13 0 6.75015599e-14
332 2 35.937 -23.68631826 -23.696705 0.005193369583 3.09718398e-14 0 1.184237893e-14
# Volume_FCC.xyz
config # atoms volume energy DFT energy energy error force DFT force force error
333 4 39.304 -19.05306013 -19.075994 0.005733468451 4.408413042e-13 0 9.403357722e-14
334 4 140.608 -34.89181942 -34.873619 0.004550104571 4.205521867e-16 0 7.995930424e-17
335 4 97.336 -44.00233081 -43.950003 0.01308195237 1.415232996e-14 0 3.16034264e-15
336 4 54.872 -41.09543073 -40.991909 0.02588043152 8.555111775e-14 0 2.113066666e-14
337 4 59.319 -43.50775941 -43.453929 0.01345760365 1.271564819e-13 0 2.918043411e-14
338 4 103.823 -42.71001322 -42.686077 0.005984056153 8.662687574e-15 0 2.033238291e-15
339 4 148.877 -33.23623171 -33.224653 0.002894676947 3.760272681e-15 0 8.828200139e-16
340 4 42.875 -26.80205403 -26.862709 0.01516374165 2.367688093e-13 0 5.576442086e-14
341 4 195.112 -25.58225558 -25.519883 0.01559314534 9.021233341e-17 0 1.300644336e-17
342 4 32.768 3.439112974 3.463071 0.005989506394 3.930877064e-13 0 8.581098794e-14
343 4 157.464 -31.61362046 -31.59595 0.004417614868 1.924212144e-15 0 4.524692264e-16
344 4 64 -45.0779547 -45.100466 0.005627824292 5.472373328e-14 0 1.295332123e-14
345 4 68.921 -46.02881414 -46.052258 0.005860964727 1.17170799e-14 0 2.588328905e-15
346 4 166.375 -30.03606118 -30.001189 0.008718044874 2.021501328e-15 0 4.889817521e-16
347 4 216 -22.76239183 -22.8504 0.02200204218 1.362657892e-17 0 1.605907726e-18
348 4 35.937 -9.17132059 -9.164691 0.001657397395 9.335605084e-13 0 1.959636157e-13
349 4 205.379 -24.16544433 -24.150343 0.003775332804 7.126234547e-17 0 9.892218775e-18
350 4 74.088 -46.43582521 -46.426795 0.002257552952 4.111390445e-14 0 1.003166541e-14
351 4 175.616 -28.50766676 -28.451145 0.01413044051 1.532300669e-14 0 4.243533957e-15
352 4 27 40.38767458 40.341566 0.01152714455 1.152275905e-12 0 2.851052558e-13
353 4 29.791 19.56248813 19.617912 0.01385596784 1.913277365e-12 0 5.114462095e-13
354 4 185.193 -27.02575709 -26.954384 0.01784327272 7.327680688e-17 0 1.026311054e-17
355 4 79.507 -46.3711418 -46.323696 0.0118614497 3.760963284e-14 0 9.767365343e-15
356 4 85.184 -45.90295967 -45.828947 0.01850316635 4.777396813e-14 0 1.033233938e-14
357 4 125 -38.2088673 -38.16029 0.01214432513 1.230604971e-14 0 3.353043138e-15
358 4 46.656 -32.88896997 -32.919741 0.007692757204 3.143002556e-13 0 6.911890042e-14
359 4 110.592 -41.29854744 -41.272675 0.006468108987 4.280348441e-14 0 1.221890865e-14
360 4 117.649 -39.80075561 -39.753322 0.01185840254 7.977033164e-15 0 1.638216837e-15
361 4 50.653 -37.5950753 -37.547435 0.01191007619 2.082774854e-13 0 4.787316377e-14
362 4 132.651 -36.55944735 -36.52595 0.008374337676 3.607358902e-15 0 8.827652613e-16
363 4 91.125 -45.09230604 -45.016087 0.0190547608 1.041675348e-14 0 2.551158559e-15
333 4 39.304 -19.0530601 -19.075994 0.00573347424 4.870371327e-13 0 1.158494597e-13
334 4 140.608 -34.89181988 -34.873619 0.004550220471 3.571521848e-16 0 6.145437519e-17
335 4 97.336 -44.0023309 -43.950003 0.01308197621 1.258804826e-14 0 3.086324954e-15
336 4 54.872 -41.09543083 -40.991909 0.02588045765 7.511529054e-14 0 1.643072252e-14
337 4 59.319 -43.50775917 -43.453929 0.01345754157 1.48328674e-13 0 3.591347416e-14
338 4 103.823 -42.71001295 -42.686077 0.005983988388 1.158954979e-14 0 2.702058254e-15
339 4 148.877 -33.23623206 -33.224653 0.002894765836 3.760274875e-15 0 8.828209033e-16
340 4 42.875 -26.80205389 -26.862709 0.01516377827 1.89090911e-13 0 4.283726152e-14
341 4 195.112 -25.58225506 -25.519883 0.01559301548 9.021076414e-17 0 1.300620875e-17
342 4 32.768 3.439113073 3.463071 0.005989481831 5.149794242e-13 0 1.212085987e-13
343 4 157.464 -31.61362058 -31.59595 0.004417644795 1.924210302e-15 0 4.524687152e-16
344 4 64 -45.07795443 -45.100466 0.005627893676 8.514576411e-14 0 2.04250796e-14
345 4 68.921 -46.02881398 -46.052258 0.005861004125 3.112390759e-14 0 6.640644387e-15
346 4 166.375 -30.036061 -30.001189 0.008718001183 2.021500767e-15 0 4.889815791e-16
347 4 216 -22.76239204 -22.8504 0.02200199108 1.362634334e-17 0 1.605879963e-18
348 4 35.937 -9.171320375 -9.164691 0.001657343655 9.474410518e-13 0 2.141435177e-13
349 4 205.379 -24.16544409 -24.150343 0.003775271327 7.126159632e-17 0 9.892077977e-18
350 4 74.088 -46.43582521 -46.426795 0.002257552775 2.937909011e-14 0 6.608476981e-15
351 4 175.616 -28.50766632 -28.451145 0.01413033122 1.241622685e-14 0 3.379996616e-15
352 4 27 40.3876743 40.341566 0.01152707469 9.429935267e-13 0 2.463954797e-13
353 4 29.791 19.56248847 19.617912 0.01385588305 1.979869349e-12 0 5.348169824e-13
354 4 185.193 -27.02575652 -26.954384 0.01784312891 7.327716062e-17 0 1.026317441e-17
355 4 79.507 -46.37114198 -46.323696 0.01186149579 3.510812338e-14 0 9.471312029e-15
356 4 85.184 -45.90296 -45.828947 0.01850324956 8.279161442e-14 0 2.294426778e-14
357 4 125 -38.2088675 -38.16029 0.01214437563 1.094273598e-14 0 3.093989755e-15
358 4 46.656 -32.88896973 -32.919741 0.007692818206 3.722873472e-13 0 9.33252318e-14
359 4 110.592 -41.29854704 -41.272675 0.006468010849 3.124001447e-14 0 8.656937841e-15
360 4 117.649 -39.8007555 -39.753322 0.01185837394 6.979305395e-15 0 1.480935345e-15
361 4 50.653 -37.59507535 -37.547435 0.01191008722 1.626035248e-13 0 4.03236472e-14
362 4 132.651 -36.55944776 -36.52595 0.008374440174 3.586800027e-15 0 8.642625101e-16
363 4 91.125 -45.09230638 -45.016087 0.01905484377 1.010713419e-14 0 2.218133085e-15

4
examples/PACKAGES/pod/Ta/Ta_training_errors.pod
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@ -4,12 +4,12 @@
---------------------------------------------------------------------------------------------------
Displaced_A15.xyz 9 576 0.000866 0.001015 0.153951 0.194173
Displaced_BCC.xyz 9 486 0.002820 0.003377 0.200656 0.252028
Displaced_FCC.xyz 9 432 0.001014 0.001184 0.084618 0.106169
Displaced_FCC.xyz 9 432 0.001014 0.001184 0.084617 0.106168
Elastic_BCC.xyz 100 200 0.000718 0.000889 0.000004 0.000005
Elastic_FCC.xyz 100 400 0.000546 0.000686 0.000135 0.000194
GSF_110.xyz 22 528 0.004675 0.005460 0.049749 0.087895
GSF_112.xyz 22 660 0.007844 0.008422 0.063553 0.103550
Liquid.xyz 3 300 0.007937 0.009923 0.348677 0.447819
Liquid.xyz 3 300 0.007937 0.009923 0.348677 0.447820
Surface.xyz 7 236 0.010462 0.014425 0.048960 0.102693
Volume_A15.xyz 30 240 0.004500 0.005556 0.000000 0.000000
Volume_BCC.xyz 21 42 0.010486 0.014233 0.000000 0.000000

25
examples/PACKAGES/pod/Ta/dump_dd
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25
examples/PACKAGES/pod/Ta/dump_ld
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@ -1,25 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
16
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 4.0000000000000000e+00
0.0000000000000000e+00 4.0000000000000000e+00
0.0000000000000000e+00 4.0000000000000000e+00
ITEM: ATOMS id c_ld[1] c_ld[2] c_ld[3] c_ld[4] c_ld[5] c_ld[6] c_ld[7] c_ld[8] c_ld[9] c_ld[10] c_ld[11] c_ld[12] c_ld[13] c_ld[14] c_ld[15] c_ld[16] c_ld[17] c_ld[18] c_ld[19] c_ld[20] c_ld[21] c_ld[22] c_ld[23] c_ld[24] c_ld[25] c_ld[26] c_ld[27] c_ld[28] c_ld[29] c_ld[30] c_ld[31] c_ld[32] c_ld[33] c_ld[34] c_ld[35] c_ld[36] c_ld[37] c_ld[38] c_ld[39] c_ld[40] c_ld[41] c_ld[42] c_ld[43] c_ld[44] c_ld[45] c_ld[46] c_ld[47] c_ld[48] c_ld[49] c_ld[50] c_ld[51] c_ld[52] c_ld[53] c_ld[54] c_ld[55] c_ld[56] c_ld[57] c_ld[58] c_ld[59] c_ld[60] c_ld[61]
1 8.86599 21.597 -18.7676 19.2641 -36.047 9.98833 78.6058 0.225652 26.2756 0.265074 15.9333 466.431 0.217335 155.681 0.382584 93.7511 352.224 3.25706 117.952 3.54203 71.8291 371.105 3.25919 125.189 4.22711 75.7691 1299.39 1.74934 435.251 2.34718 262.013 696.918 2.00063 232.959 0.674447 2.35015 0.675136 78.0954 10073.5 4.69378 3362.23 1.61977 8.26267 1.61057 1123.71 -6610.42 -61.1274 -2213.68 -21.3675 -66.4755 -20.5655 -744.709 7149 62.7853 2411.65 20.5396 81.4315 21.4563 823.333 6178.87 36664.2
2 8.91352 21.0122 -20.0392 19.0141 -33.6211 11.2016 79.4508 0.422949 26.7108 0.60572 16.2193 441.511 0.418347 147.492 0.50009 88.7894 401.571 4.02268 134.105 3.50587 82.0102 361.536 9.20638 122.002 6.82082 75.558 1130.38 3.7543 377.735 2.60159 227.282 708.186 3.76996 238.087 1.31154 5.3991 1.36466 80.6997 9277.1 8.79038 3099.12 2.94312 10.508 2.91447 1037.51 -8047.16 -80.6115 -2687.36 -27.0391 -70.2548 -26.5647 -899.108 6874.29 175.051 2319.75 62.547 129.692 61.9564 792.829 6312.43 35078.4
3 9.07817 21.5767 -17.7163 19.2161 -36.0833 9.50274 82.4132 0.378989 27.5003 0.296424 16.6666 465.554 0.148808 155.274 0.252925 93.388 313.868 5.45895 104.871 3.39856 64.9239 369.258 3.88638 123.48 4.33286 74.3833 1302.01 3.80092 434.858 2.47532 261.553 748.161 3.44052 249.653 1.11069 2.69099 1.14623 83.3946 10045.1 3.21079 3350.3 1.0439 5.45729 1.08425 1118.05 -5560.59 -96.7124 -1857.94 -33.3145 -60.21 -32.7292 -622.219 7095.69 74.681 2372.8 25.9121 83.2605 25.3364 796.021 6791.94 38367.8
4 8.34989 21.4804 -21.702 18.1332 -34.3754 11.7956 69.7207 0.0379915 23.2734 0.21755 14.0452 461.406 0.0584731 153.974 0.577297 92.6135 470.976 1.09499 157.518 1.51571 95.1392 328.812 2.42867 110.719 2.29965 67.8179 1181.67 0.986426 396.217 2.00442 239.881 582.16 0.317225 194.331 0.103269 1.81652 0.100326 64.9608 9911.18 1.25602 3307.43 0.411565 12.4006 0.429819 1104.96 -10221.1 -23.7634 -3418.45 -8.39113 -32.894 -7.85833 -1147 5962.42 44.0395 2007.7 15.9211 41.7 14.764 682.645 4860.97 32169.5
5 8.50678 21.5678 -20.8079 18.0509 -35.3966 11.6089 72.3653 0.0311681 24.161 0.148448 14.58 465.171 0.0417005 155.206 0.370962 93.2962 432.968 2.02002 145.177 2.39613 87.9422 325.836 4.90539 108.911 3.50042 65.6802 1252.92 4.18559 418.577 4.02373 252.37 615.596 0.26514 205.532 0.0892271 1.26282 0.0895989 68.7335 10032.7 0.899389 3347.46 0.310263 8.00083 0.31849 1117.96 -9009.16 -42.0323 -3020.82 -14.0737 -49.8585 -13.9072 -1018.46 5881.65 88.547 1965.94 30.8695 63.1859 29.9864 658.859 5236.74 33662.2
6 8.88963 21.5706 -18.6875 18.8352 -35.8183 10.0705 79.0255 0.269777 26.4669 0.263336 16.0472 465.292 0.189032 155.31 0.349965 93.5274 349.224 3.86444 117.13 2.96705 71.775 354.764 3.06524 118.517 4.30347 71.651 1282.95 0.606733 428.58 1.78953 258.129 702.508 2.39821 235.281 0.807793 2.34096 0.814815 79.1724 10036.6 4.07754 3350.14 1.38604 7.54895 1.36527 1119.76 -6526.15 -72.2169 -2188.87 -22.9031 -55.4468 -24.0344 -738.518 6682.04 57.7343 2232.3 19.16 81.0567 19.2354 747.416 6245.04 36770
7 8.78792 21.6715 -19.1096 17.8588 -36.6598 11.1111 77.2276 0.184298 25.8181 0.292361 15.6294 469.653 0.139435 156.779 0.584005 94.3001 365.177 2.2489 122.366 1.72086 75.1754 318.938 1.63951 106.554 1.97166 64.1938 1343.94 7.87845 448.306 5.68984 269.672 678.67 1.6196 226.887 0.548912 2.56925 0.545222 76.0671 10178.1 3.02177 3397.64 1.01493 12.6562 0.993059 1135.88 -6978.4 -42.9756 -2338.37 -14.621 -32.885 -14.2282 -787.576 5695.85 29.2798 1902.93 9.56777 35.2115 9.87979 637.202 5964.1 36270.2
8 8.57126 21.5176 -20.2996 18.8473 -36.4047 11.4339 73.4664 0.107844 24.6679 0.170497 14.9443 463.008 0.282877 154.665 0.360751 93.1367 412.073 1.77098 138.707 2.39774 84.2869 355.221 4.71338 118.799 3.92319 71.7868 1325.3 0.766534 442.995 2.42188 267.336 629.7 0.924361 211.435 0.306968 1.46137 0.320876 71.5145 9962.83 6.08684 3328.02 2.13055 7.7625 2.09158 1114.09 -8364.9 -35.9502 -2815.7 -12.8047 -48.6731 -12.1094 -956.571 6694.97 88.8345 2239.04 29.6548 73.9416 29.9329 751.337 5397.32 34015.5
9 8.68738 20.883 -21.313 19.6564 -34.0921 12.0501 75.4706 0.320461 25.3656 0.423179 15.5166 436.1 0.512785 145.749 0.462811 87.7359 454.245 3.44733 151.768 4.10355 91.7879 386.375 12.3434 131.928 9.26773 81.3727 1162.27 0.887012 390.276 1.67367 235.948 655.642 2.78397 220.36 0.992544 3.67632 1.03394 74.6685 9107.09 10.7085 3043.68 3.5307 9.6649 3.52145 1019.82 -9681.35 -73.4731 -3234.64 -24.3165 -87.4591 -23.6358 -1083.21 7594.74 242.628 2593.23 93.4017 182.17 89.1079 906.989 5695.81 32912.8
10 8.88726 21.4817 -18.8397 19.0387 -35.0694 9.95552 78.9835 0.100136 26.4637 0.403244 16.0296 461.463 0.0463147 154.123 0.724312 92.7154 354.935 0.945181 119.408 1.9192 73.8898 362.472 4.52031 121.384 3.68824 73.79 1229.86 1.86347 411.451 3.59339 248.114 701.947 0.889936 235.19 0.307487 3.58374 0.29082 79.1944 9913.01 0.994917 3310.82 0.337729 15.5595 0.3384 1107.9 -6686.88 -17.8069 -2249.61 -6.22946 -36.1572 -6.07581 -763.702 6901 86.0608 2310.99 29.0788 70.2192 28.8146 777.397 6238.39 36448
11 8.85551 20.9604 -20.5783 19.1728 -33.138 11.6017 78.42 0.397046 26.3551 0.591422 16.0971 439.339 0.256048 146.849 0.481701 88.379 423.465 2.66449 141.729 2.99435 86.5991 367.596 12.1698 124.705 9.39843 76.6795 1098.13 7.35266 367.813 5.3271 221.601 694.449 3.51604 233.388 1.22935 5.23734 1.2886 79.0654 9208.73 5.36687 3078.02 1.73028 10.0967 1.76061 1031.71 -8714.17 -54.8306 -2916.53 -17.7868 -61.6186 -18.2601 -980.175 7047.85 233.329 2390.95 86.0413 180.194 84.2878 825.369 6149.7 34453
12 8.60726 20.8375 -21.8853 19.1315 -33.469 12.4884 74.0849 0.357841 24.9489 0.457737 15.1619 434.2 0.40039 144.943 0.439226 87.0949 478.966 3.65397 160.722 3.23546 97.504 366.014 11.4707 123.452 7.8533 76.5065 1120.17 1.40609 374.496 1.77765 225.409 637.668 3.08003 214.742 1.1546 3.93986 1.15411 73.0698 9047.64 8.34312 3020.25 2.66986 9.15236 2.74761 1009.68 -10482.3 -79.9682 -3517.44 -25.805 -70.809 -25.2406 -1188.27 7002.38 219.451 2361.82 83.4582 150.245 79.6457 806.386 5488.57 32167.7
13 8.26363 21.471 -22.1293 18.0515 -35.139 12.3372 68.2876 0.0166374 22.7873 0.179346 13.7288 461.005 0.0601076 153.718 0.524162 92.3926 489.707 1.23022 163.417 1.8075 98.2847 325.858 4.62303 108.897 4.62651 65.9297 1234.75 1.79686 412.715 3.97162 248.863 564.303 0.137485 188.305 0.0458134 1.48205 0.0502254 62.9046 9898.25 1.29057 3300.49 0.429902 11.2543 0.431122 1100.88 -10836.9 -27.224 -3616.31 -9.02716 -39.9988 -8.86018 -1208.09 5882.25 83.4528 1965.76 28.226 83.5157 27.4335 658.548 4663.19 31480.9
14 9.02092 21.2084 -18.9831 19.1193 -34.1695 10.3612 81.3771 0.233268 27.353 0.37512 16.5948 449.796 0.35605 150.032 0.423853 90.1782 360.358 2.42295 121.741 2.58328 75.7884 365.548 6.36127 123.158 4.6381 75.7658 1167.55 0.157447 389.499 1.77777 233.997 734.097 2.1043 246.749 0.697062 3.38393 0.728513 83.6454 9539.46 7.55126 3181.93 2.57031 8.98924 2.56622 1062.04 -6840.72 -45.9951 -2311.03 -15.5405 -49.0388 -15.5501 -790.548 6989.02 121.623 2354.69 43.3786 88.6773 42.1955 802.132 6622.23 36603.1
15 8.77429 21.0281 -20.3511 20.5414 -32.6079 9.79667 76.9882 0.41331 25.7702 0.620366 15.6344 442.181 0.00242333 147.852 0.418274 88.9206 414.166 3.1622 138.413 3.25116 84.3004 421.951 6.9903 142.747 5.80199 88.3782 1063.27 1.05124 359.156 2.6746 217.434 675.516 3.6265 226.115 1.24317 5.44327 1.26974 76.0093 9298.22 0.050958 3109.04 0.0166354 8.7955 0.0197619 1042.74 -8428.72 -64.3541 -2816.84 -22.4697 -66.1646 -21.5318 -943.876 8667.47 143.591 2932.23 55.2809 119.181 52.1648 1006.83 5927.18 34042.7
16 8.44299 21.6032 -21.1539 17.1296 -36.122 12.7214 71.2841 0.0462392 23.8318 0.128673 14.4348 466.697 0.128065 155.827 0.290891 93.8969 447.488 1.3902 149.41 2.39914 90.4443 293.424 2.86048 98.5312 2.79516 59.7374 1304.8 0.762991 435.917 1.80361 263.055 601.851 0.390397 201.212 0.132761 1.08639 0.138592 67.4693 10082.1 2.76662 3366.36 0.92775 6.28416 0.954031 1125.92 -9466.13 -29.4082 -3160.6 -9.93853 -50.7512 -9.65067 -1057.04 5026.23 48.999 1687.8 17.1635 47.8801 15.9877 570.651 5081.42 33268.1

0
examples/PACKAGES/pod/Ta/Ta_fit.pod → examples/PACKAGES/pod/Ta/in.fitpod
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45
examples/PACKAGES/pod/Ta/in.pod Normal file
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@ -0,0 +1,45 @@
# Demonstrate POD potential for InP
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.816
units metal
# generate the box and atom positions using a FCC lattice
variable nx equal ${nrep}
variable ny equal ${nrep}
variable nz equal ${nrep}
boundary p p p
lattice bcc $a
region box block 0 ${nx} 0 ${ny} 0 ${nz}
create_box 1 box
create_atoms 1 box
mass 1 180.88
# POD potential
pair_style pod
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
# Setup output
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}

18
examples/PACKAGES/pod/Ta/Ta_compute.pod → examples/PACKAGES/pod/Ta/in.pod.compute
View File

@ -32,21 +32,21 @@ pair_coeff * *
# set up per-atom computes
compute ld all pod/atom Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod Ta Ta
compute dd all podd/atom Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod Ta Ta
compute ld all pod/atom Ta_param.pod Ta_coefficients.pod Ta Ta
compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta
# set up compute snap generating global array
compute gdd all pod/gdd Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod Ta Ta
fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector
compute gdd all pod/gdd Ta_param.pod Ta_coefficients.pod Ta Ta
#fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector
compute ldd all pod/ldd Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod Ta Ta
fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector
compute ldd all pod/ldd Ta_param.pod Ta_coefficients.pod Ta Ta
#fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector
dump mydump_ld all custom 1000 dump_ld id c_ld[*]
dump mydump_dd all custom 1000 dump_dd id c_dd[*]
#dump mydump_ld all custom 1000 dump_ld id c_ld[*]
#dump mydump_dd all custom 1000 dump_dd id c_dd[*]
variable sample_ld1 equal C_ld[1][10] # Arbitrary local descriptor
fix ldprint all print 1 "${sample_ld1}" file sample_ld.txt
fix ldprint all print 1 "${sample_ld1}"
run ${nsteps}

119
examples/PACKAGES/pod/Ta/log.22May24.fitpod.g++.1 Normal file
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
fitpod Ta_param.pod Ta_data.pod
**************** Begin of POD Potentials ****************
species: Ta
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 3
five-body radial basis functions: 2
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 28
number of local descriptors per element for five-body potential: 2
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 62
number of global descriptors: 62
**************** End of POD Potentials ****************
**************** Begin of Data File ****************
file format: extxyz
file extension: xyz
path to training data set: XYZ
path to test data set: XYZ
path to environment configuration set: XYZ
basename for output files: Ta
training fraction: 1
test fraction: 1
randomize training data set: 1
randomize test data set: 1
error analysis for training data set: 1
error analysis for test data set: 0
energy/force calculation for training data set: 0
energy/force calculation for test data set: 0
fitting weight for energy: 100
fitting weight for force: 1
fitting weight for stress: 0
save pod descriptors: 0
compute pod descriptors: 0
**************** End of Data File ****************
**************** Begin of Training Data Set ****************
---------------------------------------------------------------
data file | number of configurations | number of atoms
---------------------------------------------------------------
Displaced_A15.xyz | 9 | 576
Displaced_BCC.xyz | 9 | 486
Displaced_FCC.xyz | 9 | 432
Elastic_BCC.xyz | 100 | 200
Elastic_FCC.xyz | 100 | 400
GSF_110.xyz | 22 | 528
GSF_112.xyz | 22 | 660
Liquid.xyz | 3 | 300
Surface.xyz | 7 | 236
Volume_A15.xyz | 30 | 240
Volume_BCC.xyz | 21 | 42
Volume_FCC.xyz | 31 | 124
---------------------------------------------------------------
number of files: 12
number of configurations in all files: 363
number of atoms in all files: 4224
minimum number of atoms: 2
maximum number of atoms: 100
**************** End of Training Data Set ****************
**************** Begin of Memory Allocation ****************
maximum number of atoms in periodic domain: 100
maximum number of atoms in extended domain: 2700
maximum number of neighbors in extended domain: 270000
size of double memory: 449748
size of descriptor matrix: 62 x 62
**************** End of Memory Allocation ****************
**************** Begin of Least-Squares Fitting ****************
Configuration: # 1
Configuration: # 101
Configuration: # 201
Configuration: # 301
**************** Begin of Error Calculation ****************
Configuration: # 1
Configuration: # 101
Configuration: # 201
Configuration: # 301
**************** End of Error Calculation ****************
**************** Begin of Error Analysis for the Training Data Set ****************
---------------------------------------------------------------------------------------------------
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
---------------------------------------------------------------------------------------------------
Displaced_A15.xyz 9 576 0.000866 0.001015 0.153951 0.194173
Displaced_BCC.xyz 9 486 0.002820 0.003377 0.200656 0.252028
Displaced_FCC.xyz 9 432 0.001014 0.001184 0.084618 0.106169
Elastic_BCC.xyz 100 200 0.000718 0.000889 0.000004 0.000005
Elastic_FCC.xyz 100 400 0.000546 0.000686 0.000135 0.000194
GSF_110.xyz 22 528 0.004675 0.005460 0.049749 0.087895
GSF_112.xyz 22 660 0.007844 0.008422 0.063553 0.103550
Liquid.xyz 3 300 0.007937 0.009923 0.348677 0.447819
Surface.xyz 7 236 0.010462 0.014425 0.048960 0.102693
Volume_A15.xyz 30 240 0.004500 0.005556 0.000000 0.000000
Volume_BCC.xyz 21 42 0.010486 0.014233 0.000000 0.000000
Volume_FCC.xyz 31 124 0.010576 0.012164 0.000000 0.000000
---------------------------------------------------------------------------------------------------
All files 363 4224 0.003373 0.006207 0.096395 0.176283
---------------------------------------------------------------------------------------------------
**************** End of Error Analysis for the Training Data Set ****************
Total wall time: 0:00:00

119
examples/PACKAGES/pod/Ta/log.22May24.fitpod.g++.4 Normal file
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@ -0,0 +1,119 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
fitpod Ta_param.pod Ta_data.pod
**************** Begin of POD Potentials ****************
species: Ta
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 3
five-body radial basis functions: 2
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 28
number of local descriptors per element for five-body potential: 2
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 62
number of global descriptors: 62
**************** End of POD Potentials ****************
**************** Begin of Data File ****************
file format: extxyz
file extension: xyz
path to training data set: XYZ
path to test data set: XYZ
path to environment configuration set: XYZ
basename for output files: Ta
training fraction: 1
test fraction: 1
randomize training data set: 1
randomize test data set: 1
error analysis for training data set: 1
error analysis for test data set: 0
energy/force calculation for training data set: 0
energy/force calculation for test data set: 0
fitting weight for energy: 100
fitting weight for force: 1
fitting weight for stress: 0
save pod descriptors: 0
compute pod descriptors: 0
**************** End of Data File ****************
**************** Begin of Training Data Set ****************
---------------------------------------------------------------
data file | number of configurations | number of atoms
---------------------------------------------------------------
Displaced_A15.xyz | 9 | 576
Displaced_BCC.xyz | 9 | 486
Displaced_FCC.xyz | 9 | 432
Elastic_BCC.xyz | 100 | 200
Elastic_FCC.xyz | 100 | 400
GSF_110.xyz | 22 | 528
GSF_112.xyz | 22 | 660
Liquid.xyz | 3 | 300
Surface.xyz | 7 | 236
Volume_A15.xyz | 30 | 240
Volume_BCC.xyz | 21 | 42
Volume_FCC.xyz | 31 | 124
---------------------------------------------------------------
number of files: 12
number of configurations in all files: 363
number of atoms in all files: 4224
minimum number of atoms: 2
maximum number of atoms: 100
**************** End of Training Data Set ****************
**************** Begin of Memory Allocation ****************
maximum number of atoms in periodic domain: 100
maximum number of atoms in extended domain: 2700
maximum number of neighbors in extended domain: 270000
size of double memory: 449748
size of descriptor matrix: 62 x 62
**************** End of Memory Allocation ****************
**************** Begin of Least-Squares Fitting ****************
Configuration: # 1
Configuration: # 101
Configuration: # 201
Configuration: # 301
**************** Begin of Error Calculation ****************
Configuration: # 1
Configuration: # 101
Configuration: # 201
Configuration: # 301
**************** End of Error Calculation ****************
**************** Begin of Error Analysis for the Training Data Set ****************
---------------------------------------------------------------------------------------------------
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
---------------------------------------------------------------------------------------------------
Displaced_A15.xyz 9 576 0.000866 0.001015 0.153951 0.194173
Displaced_BCC.xyz 9 486 0.002820 0.003377 0.200656 0.252028
Displaced_FCC.xyz 9 432 0.001014 0.001184 0.084617 0.106168
Elastic_BCC.xyz 100 200 0.000718 0.000889 0.000004 0.000005
Elastic_FCC.xyz 100 400 0.000546 0.000686 0.000135 0.000194
GSF_110.xyz 22 528 0.004675 0.005460 0.049749 0.087895
GSF_112.xyz 22 660 0.007844 0.008422 0.063553 0.103550
Liquid.xyz 3 300 0.007937 0.009923 0.348677 0.447820
Surface.xyz 7 236 0.010462 0.014425 0.048960 0.102693
Volume_A15.xyz 30 240 0.004500 0.005556 0.000000 0.000000
Volume_BCC.xyz 21 42 0.010486 0.014233 0.000000 0.000000
Volume_FCC.xyz 31 124 0.010576 0.012164 0.000000 0.000000
---------------------------------------------------------------------------------------------------
All files 363 4224 0.003373 0.006207 0.096395 0.176283
---------------------------------------------------------------------------------------------------
**************** End of Error Analysis for the Training Data Set ****************
Total wall time: 0:00:00

293
examples/PACKAGES/pod/Ta/log.22May24.pod.compute.g++.1 Normal file
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@ -0,0 +1,293 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Demonstrate bispectrum computes
# initialize simulation
variable nsteps index 0
variable nrep equal 2
variable a equal 2.0
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 2
variable ny equal ${nrep}
variable ny equal 2
variable nz equal ${nrep}
variable nz equal 2
boundary p p p
atom_modify map hash
lattice bcc $a
lattice bcc 2
Lattice spacing in x,y,z = 2 2 2
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 2 0 ${ny} 0 ${nz}
region box block 0 2 0 2 0 ${nz}
region box block 0 2 0 2 0 2
create_box 2 box
Created orthogonal box = (0 0 0) to (4 4 4)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 16 atoms
using lattice units in orthogonal box = (0 0 0) to (4 4 4)
create_atoms CPU = 0.002 seconds
mass * 180.88
displace_atoms all random 0.1 0.1 0.1 123456
Displacing atoms ...
# set up dummy potential to satisfy cutoff
variable rcutfac equal 6.0
pair_style zero ${rcutfac}
pair_style zero 6
pair_coeff * *
# set up per-atom computes
compute ld all pod/atom Ta_param.pod Ta_coefficients.pod Ta Ta
**************** Begin of POD Potentials ****************
species: Ta
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 3
five-body radial basis functions: 2
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 28
number of local descriptors per element for five-body potential: 2
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 62
number of global descriptors: 62
**************** End of POD Potentials ****************
**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 62
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************
compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta
**************** Begin of POD Potentials ****************
species: Ta
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 3
five-body radial basis functions: 2
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 28
number of local descriptors per element for five-body potential: 2
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 62
number of global descriptors: 62
**************** End of POD Potentials ****************
**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 62
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************
# set up compute snap generating global array
compute gdd all pod/gdd Ta_param.pod Ta_coefficients.pod Ta Ta
**************** Begin of POD Potentials ****************
species: Ta
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 3
five-body radial basis functions: 2
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 28
number of local descriptors per element for five-body potential: 2
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 62
number of global descriptors: 62
**************** End of POD Potentials ****************
**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 62
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************
#fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector
compute ldd all pod/ldd Ta_param.pod Ta_coefficients.pod Ta Ta
**************** Begin of POD Potentials ****************
species: Ta
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 3
five-body radial basis functions: 2
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 28
number of local descriptors per element for five-body potential: 2
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 62
number of global descriptors: 62
**************** End of POD Potentials ****************
**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 62
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************
#fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector
#dump mydump_ld all custom 1000 dump_ld id c_ld[*]
#dump mydump_dd all custom 1000 dump_dd id c_dd[*]
variable sample_ld1 equal C_ld[1][10] # Arbitrary local descriptor
fix ldprint all print 1 "${sample_ld1}" file sample_ld.txt
run ${nsteps}
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: More than one compute pod (src/ML-POD/compute_pod_atom.cpp:87)
WARNING: More than one compute pod (src/ML-POD/compute_podd_atom.cpp:87)
WARNING: More than one compute pod (src/ML-POD/compute_pod_global.cpp:87)
WARNING: More than one compute pod (src/ML-POD/compute_pod_local.cpp:89)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8
ghost atom cutoff = 8
binsize = 4, bins = 1 1 1
5 neighbor lists, perpetual/occasional/extra = 1 4 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute pod/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute podd/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute pod/gdd, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(5) compute pod/ldd, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
0.265074145878138
Per MPI rank memory allocation (min/avg/max) = 6.326 | 6.326 | 6.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0
Loop time of 3.232e-06 on 1 procs for 0 steps with 16 atoms
154.7% 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 | | 3.232e-06 | | |100.00
Nlocal: 16 ave 16 max 16 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1984 ave 1984 max 1984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4311 ave 4311 max 4311 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 8623 ave 8623 max 8623 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8623
Ave neighs/atom = 538.9375
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

154
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@ -0,0 +1,154 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Demonstrate POD potential for InP
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.816
units metal
# generate the box and atom positions using a FCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.816
Lattice spacing in x,y,z = 3.816 3.816 3.816
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (15.264 15.264 15.264)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
using lattice units in orthogonal box = (0 0 0) to (15.264 15.264 15.264)
create_atoms CPU = 0.001 seconds
mass 1 180.88
# POD potential
pair_style pod
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
**************** Begin of POD Potentials ****************
species: Ta
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 3
five-body radial basis functions: 2
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 28
number of local descriptors per element for five-body potential: 2
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 62
number of global descriptors: 62
**************** End of POD Potentials ****************
**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 62
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************
# Setup output
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6
ghost atom cutoff = 6
binsize = 3, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair pod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.208 | 3.208 | 3.208 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.361449 0 -10.322974 -354249.12
10 300.08332 -10.361459 0 -10.322974 -354201.89
20 300.33492 -10.361492 0 -10.322974 -354060.15
30 300.76425 -10.361547 0 -10.322974 -353823.72
40 301.39008 -10.361627 0 -10.322974 -353492.3
50 302.24056 -10.361736 0 -10.322974 -353065.43
60 303.35321 -10.361879 0 -10.322974 -352542.47
70 304.77506 -10.362061 0 -10.322974 -351922.54
80 306.56275 -10.36229 0 -10.322974 -351204.53
90 308.78281 -10.362575 0 -10.322974 -350386.99
100 311.51191 -10.362925 0 -10.322974 -349468.1
Loop time of 0.262752 on 1 procs for 100 steps with 128 atoms
Performance: 16.441 ns/day, 1.460 hours/ns, 380.587 timesteps/s, 48.715 katom-step/s
97.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26055 | 0.26055 | 0.26055 | 0.0 | 99.16
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0007928 | 0.0007928 | 0.0007928 | 0.0 | 0.30
Output | 0.00029978 | 0.00029978 | 0.00029978 | 0.0 | 0.11
Modify | 0.00047709 | 0.00047709 | 0.00047709 | 0.0 | 0.18
Other | | 0.0006355 | | | 0.24
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 727 ave 727 max 727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3328 ave 3328 max 3328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3328
Ave neighs/atom = 26
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

154
examples/PACKAGES/pod/Ta/log.22May24.pod.g++.4 Normal file
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@ -0,0 +1,154 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-176-gc2e4ad220f-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Demonstrate POD potential for InP
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.816
units metal
# generate the box and atom positions using a FCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.816
Lattice spacing in x,y,z = 3.816 3.816 3.816
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (15.264 15.264 15.264)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
using lattice units in orthogonal box = (0 0 0) to (15.264 15.264 15.264)
create_atoms CPU = 0.002 seconds
mass 1 180.88
# POD potential
pair_style pod
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
**************** Begin of POD Potentials ****************
species: Ta
periodic boundary conditions: 1 1 1
number of environment clusters: 1
number of principal compoments: 2
inner cut-off radius: 1
outer cut-off radius: 5
bessel polynomial degree: 4
inverse polynomial degree: 8
one-body potential: 1
two-body radial basis functions: 6
three-body radial basis functions: 5
three-body angular degree: 4
four-body radial basis functions: 4
four-body angular degree: 3
five-body radial basis functions: 2
five-body angular degree: 0
six-body radial basis functions: 0
six-body angular degree: 0
seven-body radial basis functions: 0
seven-body angular degree: 0
number of local descriptors per element for one-body potential: 1
number of local descriptors per element for two-body potential: 6
number of local descriptors per element for three-body potential: 25
number of local descriptors per element for four-body potential: 28
number of local descriptors per element for five-body potential: 2
number of local descriptors per element for six-body potential: 0
number of local descriptors per element for seven-body potential: 0
number of local descriptors per element for all potentials: 62
number of global descriptors: 62
**************** End of POD Potentials ****************
**************** Begin of Model Coefficients ****************
total number of coefficients for POD potential: 62
total number of elements for PCA projection matrix: 0
total number of elements for PCA centroids: 0
**************** End of Model Coefficients ****************
# Setup output
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6
ghost atom cutoff = 6
binsize = 3, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair pod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.188 | 3.188 | 3.188 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.361449 0 -10.322974 -354249.12
10 300.08332 -10.361459 0 -10.322974 -354201.89
20 300.33492 -10.361492 0 -10.322974 -354060.15
30 300.76425 -10.361547 0 -10.322974 -353823.72
40 301.39008 -10.361627 0 -10.322974 -353492.3
50 302.24056 -10.361736 0 -10.322974 -353065.43
60 303.35321 -10.361879 0 -10.322974 -352542.47
70 304.77506 -10.362061 0 -10.322974 -351922.54
80 306.56275 -10.36229 0 -10.322974 -351204.53
90 308.78281 -10.362575 0 -10.322974 -350386.99
100 311.51191 -10.362925 0 -10.322974 -349468.1
Loop time of 0.134056 on 4 procs for 100 steps with 128 atoms
Performance: 32.225 ns/day, 0.745 hours/ns, 745.959 timesteps/s, 95.483 katom-step/s
90.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10115 | 0.10421 | 0.10541 | 0.5 | 77.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.024822 | 0.026183 | 0.029671 | 1.3 | 19.53
Output | 0.00057395 | 0.00094904 | 0.0011461 | 0.0 | 0.71
Modify | 0.00037802 | 0.00041906 | 0.00046194 | 0.0 | 0.31
Other | | 0.002294 | | | 1.71
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 431 ave 431 max 431 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 832 ave 832 max 832 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3328
Ave neighs/atom = 26
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

53
examples/PACKAGES/pod/Ta/pod.gdd.dat
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@ -1,53 +0,0 @@
# Time-averaged data for fix gdd
# TimeStep Number-of-rows
# Row c_gdd[1] c_gdd[2] c_gdd[3] c_gdd[4] c_gdd[5] c_gdd[6] c_gdd[7] c_gdd[8] c_gdd[9] c_gdd[10] c_gdd[11] c_gdd[12] c_gdd[13] c_gdd[14] c_gdd[15] c_gdd[16] c_gdd[17] c_gdd[18] c_gdd[19] c_gdd[20] c_gdd[21] c_gdd[22] c_gdd[23] c_gdd[24] c_gdd[25] c_gdd[26] c_gdd[27] c_gdd[28] c_gdd[29] c_gdd[30] c_gdd[31] c_gdd[32] c_gdd[33] c_gdd[34] c_gdd[35] c_gdd[36] c_gdd[37] c_gdd[38] c_gdd[39] c_gdd[40] c_gdd[41] c_gdd[42] c_gdd[43] c_gdd[44] c_gdd[45] c_gdd[46] c_gdd[47] c_gdd[48] c_gdd[49] c_gdd[50] c_gdd[51] c_gdd[52] c_gdd[53] c_gdd[54] c_gdd[55] c_gdd[56] c_gdd[57] c_gdd[58] c_gdd[59] c_gdd[60] c_gdd[61] c_gdd[62]
0 49
1 16 139.502 341.467 -322.364 301.061 -558.213 178.025 1217.17 3.54361 407.75 5.4385 247.263 7288.81 3.25819 2433.47 7.14381 1464.12 6521.41 42.6546 2184.43 43.7376 1331.68 5674.71 94.4435 1908.97 79.4486 1165 19499.4 39.0061 6523.84 45.9529 3932.66 10627.4 31.2643 3560.23 10.7556 47.7241 11.0114 1198.66 155612 69.1093 51952.9 23.0733 152.394 23.1467 17372.6 -132455 -848.45 -44364.2 -285.628 -878.695 -280.802 -14929.1 107147 1800.09 36049.6 650.201 1511.56 632.185 12243.9 92853.9 554374
2 0 -1.71226 1.18644 -5.72168 -14.2026 -10.1111 10.4063 -32.219 -3.14334 -12.6834 -1.51144 -8.71421 51.7426 -2.24368 11.0928 -2.35072 2.00007 161.166 -21.4398 45.2831 -10.8518 25.1564 -544.687 45.2932 -196.537 15.6181 -126.407 713.847 -33.5197 226.798 -27.8508 121.565 -452.454 -28.9448 -168.077 -9.71677 -14.666 -9.83593 -67.68 1691.56 -47.6884 432.813 -16.8424 -49.1279 -17.217 56.613 -2835.97 343.276 -787.033 117.304 172.352 117.571 -162.197 -15671.4 802.994 -5524.96 260.235 236.565 251.337 -2050.27 -5623.99 -10983.1
3 0 -1.27018 3.71202 -0.730237 -17.6979 -20.9172 11.0011 -22.0578 -1.335 -7.30524 -3.167 -4.10006 159.891 1.60171 53.7177 -1.31133 33.0622 47.6669 -27.3828 14.3183 -29.6384 7.81344 -669.842 -64.6081 -221.594 -39.9412 -135.75 1482.57 -6.64938 486.591 -6.25031 293.817 -287.317 -12.0359 -95.4859 -3.95967 -28.4545 -4.41944 -31.4222 5165.57 34.9674 1731.93 11.419 -26.3519 11.4917 583.869 -2004.41 549.125 -638.514 187.605 586.353 173.659 -187.908 -19032.2 -1285.21 -6326.45 -415.12 -822.517 -432.244 -2093.11 -3326.85 2373.82
4 0 1.20718 -2.15286 2.54518 15.3568 11.5486 -10.9218 21.59 1.48802 8.44632 1.01294 6.0115 -92.5985 -1.64272 -29.4332 0.426649 -15.0188 -105.828 12.6939 -22.4745 8.2745 -11.228 595.473 2.87678 207.299 17.7254 134.319 -806.053 28.4463 -251.882 19.4721 -143.174 289.342 13.2275 107.721 4.89179 9.44382 4.70798 43.4013 -2987.33 -35.3818 -965.872 -11.932 8.10691 -11.9024 -302.078 3319.73 -252.785 853.39 -73.4214 -144.876 -79.4044 116.399 17299.7 149.827 5956.66 38.3742 423.534 50.6902 2111.62 3444.06 2327.58
5 0 -1.99803 6.61653 6.26013 -10.5883 -27.7148 -0.62483 -36.1278 -2.42942 -14.2557 -3.5189 -10.4623 278.861 -2.80108 89.3829 -1.60973 51.1707 -268.941 7.60678 -88.6845 0.241063 -53.1507 -391.569 -43.8113 -139.297 -46.4853 -97.1746 1900.06 3.10574 623.485 -10.7555 372.264 -489.536 -22.7284 -183.234 -8.4627 -32.5786 -8.99636 -74.3883 8815.53 -56.7119 2864.86 -18.6646 -31.117 -18.7669 905.804 8634.54 -135.499 2861.43 -56.3989 27.2906 -48.2942 942.058 -10857.4 -920.098 -3793.92 -339.664 -944.304 -336.895 -1383.39 -5891.85 5877.17
6 0 3.0412 -7.13113 0.508789 21.2402 24.5232 -9.08227 54.8382 5.8606 20.3144 6.37212 13.2025 -300.791 5.38744 -97.8446 8.39789 -58.1172 1.2467 38.2501 2.2908 26.8241 -1.51967 810.399 38.5926 266.303 48.9855 169.576 -1665.91 19.0666 -542.91 26.4995 -324.79 741.239 53.5828 265.693 19.2272 58.163 19.5523 101.069 -9516.44 111.589 -3123.08 36.6414 175.549 36.5985 -1007.94 -645.642 -722.208 -255.819 -249.804 -507.677 -242.313 -110.426 23203.9 907.753 7683.61 326.71 1066.66 319.894 2524.49 8901.8 668.962
7 0 -0.531556 4.06847 11.5973 11.8798 4.39191 -24.9162 -8.94187 -1.32612 -3.59025 -1.75803 -3.41671 170.163 -1.48152 56.0589 0.413438 32.3316 -431.93 22.7707 -142.834 20.3704 -79.3855 456.37 -8.43561 130.86 4.48822 70.787 -304.244 -48.4603 -126.147 -33.6793 -89.3064 -112.484 -12.1355 -43.3799 -5.25111 -16.3999 -5.65167 -18.3648 5337.2 -28.7704 1767.85 -7.89398 11.8103 -8.00378 582.757 12042.6 -405.605 3999.39 -137.193 -370.558 -133.112 1320.99 13163.2 -97.1505 3992.31 -109.024 140.954 -90.9239 1052.99 -1253.5 10352.1
8 0 2.74376 -4.98831 5.15245 28.8349 30.4984 -20.2633 50.4944 4.10007 18.8177 4.38325 12.1746 -214.108 0.307813 -67.0293 3.72786 -38.0271 -150.701 44.5051 -44.8579 37.6474 -26.9595 1102.5 60.1074 368.663 43.5134 230.656 -2152.34 18.6493 -707.723 17.9426 -421.246 695.628 37.8876 249.736 12.5135 40.3533 13.2435 95.1333 -6893.23 5.47808 -2205.76 2.0604 77.7196 2.98481 -673.99 2893.06 -806.712 862.82 -278.94 -699.673 -267.048 218.839 31625 1291.64 10585.2 420.043 967.567 422.537 3558.58 8503.95 6193.78
9 0 0.640608 0.0146049 2.88415 4.29522 -2.13348 -1.11688 11.4403 1.43383 4.42707 -0.0100667 3.52629 0.267156 1.25348 1.58617 2.42861 3.29321 -97.7102 12.1899 -26.437 1.80988 -14.5195 162.106 -66.1861 67.325 -19.9454 42.3313 143.105 17.8452 53.3579 17.1417 36.9065 153.33 12.6625 56.4793 4.48579 -0.401078 4.25059 22.5197 -2.84484 26.8272 31.5587 9.15047 51.7154 9.39432 32.2329 2412.95 -222.877 688.778 -84.607 -24.3502 -81.9307 152.237 4573.6 -1248.87 1774 -449.845 -361.086 -415.842 764.72 1827.87 5683.23
10 0 -1.52616 3.40335 -2.09757 -15.7506 -9.43124 8.04783 -27.1519 -2.78101 -10.3831 -1.9021 -7.10569 145.793 2.44536 48.2985 -1.63452 27.5727 85.1319 -25.5721 17.4925 -13.7573 8.76856 -601.295 -7.84448 -214.192 -32.7627 -142.012 673.879 -4.83628 209.024 -6.10774 123.82 -362.485 -25.6104 -132.669 -9.43487 -17.4975 -9.20263 -51.9285 4685.01 53.016 1555.64 17.6317 -34.1121 17.5455 514.521 -2593.95 475.704 -650.457 150.049 254.87 156.385 -76.0431 -17230.9 -252.058 -6019.31 -67.6741 -711.316 -86.9269 -2191.61 -4303.78 -807.445
11 0 -0.916136 2.40014 -1.38124 -17.8105 -20.8895 14.3461 -15.0604 0.0259635 -4.62048 -2.2469 -3.09715 102.707 -1.22472 36.5669 -3.52485 22.7972 76.8201 -17.1947 18.6581 -21.383 6.68712 -666.155 -43.0753 -229.769 -11.8224 -146.212 1453.04 -23.6663 475.235 -17.2002 288.825 -185.221 0.495168 -58.3878 0.442337 -19.3529 0.336784 -17.1623 3296.79 -25.3272 1149.4 -7.13509 -73.8676 -7.69495 416.904 -2955.21 357.358 -844.982 136.093 427.593 123.475 -187.729 -18724.2 -879.304 -6413.61 -280.586 -286.397 -275.198 -2249.37 -2019.05 769.646
12 0 0.490027 -0.741764 0.986647 7.45855 14.2662 -8.78368 9.15998 -0.0988179 2.98464 1.33543 2.03385 -31.754 1.70524 -8.78574 2.02962 -4.29361 -21.2154 -17.8662 -10.3865 -4.78538 -5.98063 286.031 22.9748 107.735 6.31416 72.2589 -995.247 -14.526 -322.505 -0.738772 -188.124 127.832 -0.665673 42.1909 -0.0707228 11.6685 -0.298358 13.702 -1019.66 36.4482 -302.047 12.2409 43.0567 11.9308 -75.3091 99.2829 367.391 102.009 115.242 109.668 117.396 79.9121 8245 453.84 2993.45 154.785 141.513 142.608 1161.37 1579.54 1852.07
13 0 0.37776 0.221181 2.33071 4.4966 7.56891 -7.76065 6.8062 -0.0815566 3.11051 0.134582 2.12171 9.53988 3.85398 5.76546 2.31128 4.90635 -72.0485 -13.4333 -21.704 -9.45771 -10.6354 170.881 0.587047 64.7892 4.52624 41.6551 -529.321 -7.76953 -172.904 -5.37533 -98.4419 91.9653 -1.01939 37.9367 -0.429224 0.908315 -0.451243 17.7129 308.762 81.2597 157.803 26.6759 49.1619 26.4973 89.6278 1555.13 267.351 476.705 90.6937 191.586 87.641 130.435 4875.44 9.63979 1784.05 30.3668 87.3979 20.2535 716.761 1104.55 4410.39
14 0 0.798816 -2.77115 0.976132 20.2624 18.5938 -14.9692 12.3815 0.231409 3.89383 1.72379 2.46808 -119.295 -2.28627 -43.314 1.57561 -26.7271 -74.4515 31.3442 -20.0856 28.3389 -11.4825 742.847 51.1614 248.982 25.5107 158.005 -1311.48 -1.66915 -422.594 5.05656 -256.493 141.827 1.73302 45.3148 0.593481 14.584 0.728743 13.8016 -3851.69 -49.3618 -1360.3 -16.333 32.9032 -16.6841 -504.507 3308.78 -643.889 1009.19 -217.859 -581.38 -208.511 273.159 20448.6 1034.29 6848.3 381.919 540.576 356.627 2302.85 1416.52 -3080.31
15 0 -0.741996 1.73418 -1.10928 -13.1259 -19.813 12.8203 -13.0665 -0.325837 -4.70584 -1.44859 -2.93759 73.9783 -1.09844 23.6504 -2.34293 14.2212 24.1912 5.01978 7.40005 -3.88683 3.54626 -484.753 -29.9707 -168.082 -17.5196 -107.064 1386.63 18.6252 445.399 9.43615 262.951 -172.598 -2.71354 -60.6142 -1.07493 -12.3723 -0.964495 -22.3242 2367.34 -23.4512 767.913 -8.18451 -49.6024 -7.88579 241.869 -92.3504 -88.7983 -19.784 -28.0913 76.7181 -31.4575 -1.38423 -13444.5 -654.734 -4606.57 -241.513 -398.394 -221.937 -1617.54 -2026.92 -867.526
16 0 -0.372246 0.975509 -0.839743 -11.4258 -9.01447 10.4901 -5.76355 0.174164 -2.95877 0.438347 -2.32213 41.7925 0.611914 14.2277 1.54308 7.15601 45.7004 -8.45185 4.78009 -4.13162 4.11594 -422.968 -33.5041 -139.29 -26.792 -86.8866 624.531 -7.96431 202.399 -6.61835 123.625 -66.0888 1.6607 -30.9924 0.508964 4.02753 0.429973 -16.3164 1343.07 13.1926 454.152 4.03357 33.2714 4.25857 155.642 -1756.53 193.023 -369.313 45.0093 99.7628 52.8619 21.0657 -11743.8 -676.051 -3885.33 -267.699 -534.43 -243.764 -1274.9 -662.706 253.544
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43 0 -0.347463 -1.74948 -10.2265 -17.9637 -13.7608 26.0206 -6.71702 0.00353559 -2.01042 0.00642563 -0.962177 -72.8645 -0.552821 -25.705 -2.78329 -16.3519 365.439 -20.5195 118.465 -20.6171 64.68 -669.464 43.1347 -212.495 12.8716 -123.903 971.869 5.95807 336.502 4.60171 206.768 -96.5751 0.0550831 -29.841 0.581951 0.320846 0.965128 -8.20024 -2274.86 -12.1818 -789.461 -4.41215 -59.8836 -4.79579 -284.862 -9695.3 351.664 -3177.19 127.791 369.05 130.221 -1025.93 -18709.5 758.391 -6039.05 327.261 190.405 309.632 -1869.66 -1225.81 -9681.96
44 0 1.81607 -4.60233 -2.20061 8.98917 19.6259 -3.05995 33.2588 1.61194 13.7713 2.4339 10.0444 -194.331 3.69497 -59.1161 1.8142 -31.8685 106.948 -21.7538 38.751 -13.6532 24.6549 363.774 29.8915 138.805 38.891 97.5572 -1324.95 9.6874 -422.1 14.4709 -242.63 456.024 14.8891 176.173 5.24378 22.6 5.72405 75.1022 -6154.35 77.911 -1932.22 26.3085 37.1709 25.92 -565.21 -3773.22 427.271 -1317.26 143.007 263.329 139.333 -478.328 11001.2 635.116 4027.23 252.594 798.528 238.706 1594.07 5549.25 -562.095
45 0 -2.28383 5.71347 1.39389 -16.9199 -25.301 5.71186 -40.3047 -2.66191 -14.3527 -4.93071 -9.70116 241.361 -4.85049 79.3619 -6.39618 47.5119 -54.52 -12.3778 -16.8126 -17.4809 -11.2581 -657.178 -52.7957 -233.359 -45.2823 -153.699 1703.67 -35.398 559.255 -24.636 333.821 -533.737 -24.0955 -186.278 -8.13845 -44.1344 -8.60176 -67.9859 7647.63 -101.86 2527.3 -33.7212 -133.939 -33.6319 828.011 1603.79 251.51 515.3 101.404 352.198 82.2715 161.95 -19221.2 -1116.39 -6715.87 -395.635 -956.34 -388.434 -2440.55 -6285.82 536.379
46 0 -2.08239 4.71136 1.1566 -14.193 -15.7643 3.71861 -36.9667 -3.46806 -14.2982 -3.28243 -9.98848 198.709 -3.49483 62.7812 -3.33413 35.3873 -46.8656 -9.07879 -25.1851 -6.19032 -16.989 -544.465 -26.061 -195.345 -27.4887 -127.374 1062.75 -49.8142 329.114 -26.7181 188.867 -492.348 -31.1283 -181.907 -11.899 -29.9271 -11.3636 -72.8378 6285.46 -73.3022 2023.15 -24.1081 -69.4101 -24.1281 626.329 1419.39 195.685 661.611 50.9512 136.971 62.0284 344.904 -15751.8 -594.446 -5542.4 -245.772 -599.603 -236.364 -2051.84 -5830.86 -994.268
47 0 0.522636 -0.067163 1.89477 -0.88386 -2.89163 2.38384 9.98143 1.62545 4.25047 -0.0796047 3.20772 -2.4561 1.92247 1.64014 0.353972 2.96617 -50.8576 14.1349 -15.9229 5.2009 -6.11197 -15.8043 -21.6047 -16.8806 6.76501 -14.1515 209.378 9.48013 51.885 4.36444 26.5115 141.75 14.6417 55.3639 4.90848 -0.152061 4.99267 23.8357 -65.5993 41.2769 30.4906 14.9549 7.61959 14.4725 44.9648 765.289 -283.839 234.628 -84.7862 -108.593 -86.0147 62.1286 71.906 -392.025 -189.948 -146.88 128.156 -124.61 -214.033 1776.78 4398.41
48 0 0.897917 -2.54751 2.55785 19.2035 21.3915 -16.9319 14.7353 0.292086 4.75312 1.95445 3.13352 -108.974 -0.206422 -37.4117 2.34789 -22.5424 -117.802 29.178 -36.3138 27.19 -19.2897 695.297 32.0485 232.811 8.71269 145.338 -1506.12 -13.5142 -496.603 -2.16286 -301.831 180.904 2.60858 58.7905 0.482766 17.2001 0.907472 18.5889 -3496.85 -5.05099 -1189.52 -1.70555 49.0581 -1.56906 -412.065 3989.57 -583.746 1269.43 -212.013 -555.668 -195.127 380.752 18959.6 685.915 6356.17 235.724 251.28 222.109 2143.24 1968.47 -1171.56
49 0 -0.220961 -0.948372 -3.58304 1.08001 4.45625 2.57092 -4.22096 -0.961047 -2.08315 -0.118499 -0.953615 -41.352 -3.20948 -16.7826 -2.69925 -10.4931 117.124 -0.247009 40.6346 5.73642 24.6245 45.1734 21.4611 13.8275 7.4414 6.57662 -314.81 16.4057 -111.851 15.6483 -71.1075 -59.9264 -8.03309 -25.8428 -2.76361 -0.730972 -2.68206 -12.5968 -1351.74 -68.4205 -514.525 -23.0659 -57.803 -22.6362 -214.599 -2728.9 9.07232 -947.878 2.68987 -118.088 2.7814 -339.058 1423.97 376.878 447.508 131.732 130.497 126.311 126.461 -750.755 -5556.53

53
examples/PACKAGES/pod/Ta/pod.ldd.dat
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2
examples/PACKAGES/pod/Ta/sample_ld.txt
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@ -1,2 +0,0 @@
# Fix print output for fix ldprint
0.265074145878138

63
examples/PACKAGES/pod/test/Ta_coeff.pod Normal file
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@ -0,0 +1,63 @@
model_coefficients: 62 0 0
-3.495093
-59.701906
30.663456
10.791538
0.840297
0.730228
0.910582
-67.196938
-179.985939
524.691284
670.837805
-259.035435
3.823252
52.397945
-63.764311
-120.411099
39.425094
1.642051
-10.593072
0.363492
16.232118
-2.165456
0.014326
0.691317
1.208074
-1.186301
-0.656701
0.011029
-0.044294
-0.042611
0.025912
-0.035474
-5.179647
428.614009
-16.386364
126.893554
-410.027777
-953.238514
-18.330799
1.006988
-22.929962
-0.914978
-4.986332
29.072433
31.345932
0.723031
0.249736
-1.438448
-0.632864
0.148064
2.642487
-0.405224
0.104130
0.107113
-0.020909
-0.498780
0.247484
0.093056
-0.271642
0.355028
1.479538
-0.216955

63
examples/PACKAGES/pod/test/Ta_coefficients.pod Normal file
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@ -0,0 +1,63 @@
model_coefficients: 62 0 0
-3.495093
-59.701906
30.663456
10.791538
0.840297
0.730228
0.910582
-67.196938
-179.985939
524.691284
670.837805
-259.035435
3.823252
52.397945
-63.764311
-120.411099
39.425094
1.642051
-10.593072
0.363492
16.232118
-2.165456
0.014326
0.691317
1.208074
-1.186301
-0.656701
0.011029
-0.044294
-0.042611
0.025912
-0.035474
-5.179647
428.614009
-16.386364
126.893554
-410.027777
-953.238514
-18.330799
1.006988
-22.929962
-0.914978
-4.986332
29.072433
31.345932
0.723031
0.249736
-1.438448
-0.632864
0.148064
2.642487
-0.405224
0.104130
0.107113
-0.020909
-0.498780
0.247484
0.093056
-0.271642
0.355028
1.479538
-0.216955

2
examples/PACKAGES/pod/Ta/Ta_mdrun.pod → examples/PACKAGES/pod/test/Ta_mdrun.pod
View File

@ -24,7 +24,7 @@ mass 1 180.88
# POD potential
pair_style pod
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod Ta
pair_coeff * * Ta_param.pod Ta_coeff.pod Ta
# Setup output

46
examples/PACKAGES/pod/test/Ta_param.pod Normal file
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@ -0,0 +1,46 @@
# chemical element symbols
species Ta
# periodic boundary conditions
pbc 1 1 1
# inner cut-off radius
rin 1.0
# outer cut-off radius
rcut 5.0
# use only for enviroment-adaptive potentials
number_of_environment_clusters 1
# principal_components of local descriptors
number_of_principal_components 2
# polynomial degrees for radial basis functions
bessel_polynomial_degree 4
inverse_polynomial_degree 8
# two-body linear POD potential
twobody_number_radial_basis_functions 6
# three-body linear POD potential
threebody_number_radial_basis_functions 5
threebody_angular_degree 4
# four-body linear POD potential
fourbody_number_radial_basis_functions 4
fourbody_angular_degree 3
# five-body linear POD potential
fivebody_number_radial_basis_functions 2
fivebody_angular_degree 0
# six-body linear POD potential
sixbody_number_radial_basis_functions 0
sixbody_angular_degree 0
# seven-body linear POD potential
sevenbody_number_radial_basis_functions 0
sevenbody_angular_degree 0

164
examples/PACKAGES/pod/test/data.manybody Normal file
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@ -0,0 +1,164 @@
LAMMPS data file via write_data, version 5 May 2020, timestep = 0
64 atoms
8 atom types
0.0000000000000000e+00 1.0862000000000000e+01 xlo xhi
0.0000000000000000e+00 1.0862000000000000e+01 ylo yhi
0.0000000000000000e+00 1.0862000000000000e+01 zlo zhi
Masses
1 28.06
2 28.06
3 28.06
4 28.06
5 28.06
6 28.06
7 28.06
8 28.06
Pair Coeffs # zero
1
2
3
4
5
6
7
8
Atoms # atomic
1 1 1.0821582679234250e+01 1.0768089890052606e+01 5.2782114154092112e-02 -1 -1 0
2 2 1.2644623589070805e-01 2.6973866151300663e+00 2.6838404910230733e+00 0 0 0
3 3 2.6886015615971299e+00 1.0779945762964871e+01 2.8299381505970089e+00 0 -1 0
4 4 2.8329007005604918e+00 2.6690743201866627e+00 1.2359937723893642e-01 0 0 0
5 5 1.5213921972716424e+00 1.2921595444932625e+00 1.3789642982618950e+00 0 0 0
6 6 1.4860425041058531e+00 3.8853665070739183e+00 3.9153843913498028e+00 0 0 0
7 7 4.1419871594220101e+00 1.4231884057342254e+00 3.8965351751257127e+00 0 0 0
8 8 4.0916002382684269e+00 4.0857045774480580e+00 1.4818331695143521e+00 0 0 0
9 1 5.4332483929070872e+00 1.8873958941024710e-01 1.4627921802284161e-01 0 0 0
10 2 5.4368414340977749e+00 2.8924828813043342e+00 2.8667860819470539e+00 0 0 0
11 3 8.1119493800203539e+00 1.0773000209952240e-01 2.5336452866728161e+00 0 0 0
12 4 8.2955426243976884e+00 2.8748882519562673e+00 3.8350628986186623e-02 0 0 0
13 5 6.7320798601505025e+00 1.3027095494870840e+00 1.4928982294197886e+00 0 0 0
14 6 6.8742317689794499e+00 3.9653412376102484e+00 4.0506805154464347e+00 0 0 0
15 7 9.6779045786138891e+00 1.1702527636124300e+00 4.0071980341104547e+00 0 0 0
16 8 9.4540589455765716e+00 4.1121983054349887e+00 1.1619194458593471e+00 0 0 0
17 1 1.0803705461284940e+01 5.2746878159845654e+00 6.1123252595366578e-02 -1 0 0
18 2 1.4726683047938480e-01 8.0601198670201093e+00 2.5246050069821555e+00 0 0 0
19 3 2.7558004708887545e+00 5.5610142272980951e+00 2.6646181990826121e+00 0 0 0
20 4 2.9144739608014811e+00 8.3018591904953851e+00 1.0783914655958263e+01 0 0 -1
21 5 1.2910071356246513e+00 6.6414284435159896e+00 1.3243501732305625e+00 0 0 0
22 6 1.4393274075135483e+00 9.3757380802070216e+00 4.1734140393865129e+00 0 0 0
23 7 3.8748234996653967e+00 6.6345588763271506e+00 4.1830344304096814e+00 0 0 0
24 8 4.0077815606028455e+00 9.5761890520229667e+00 1.2373973499758391e+00 0 0 0
25 1 5.3669071758277278e+00 5.4229041366278681e+00 1.0794824304575485e+01 0 0 -1
26 2 5.4196958007648099e+00 8.1568234541650497e+00 2.6217941520038499e+00 0 0 0
27 3 8.1026284023132771e+00 5.2810576792517949e+00 2.6349151849110681e+00 0 0 0
28 4 8.1262346520143254e+00 7.9467964047716446e+00 1.0843674997034331e+01 0 0 -1
29 5 6.9361807905637809e+00 6.6580470054546828e+00 1.4325206768451122e+00 0 0 0
30 6 6.9233840741657815e+00 9.4991345042823276e+00 4.0971134730800349e+00 0 0 0
31 7 9.6892812976096909e+00 6.6097689260640271e+00 3.9383403581013390e+00 0 0 0
32 8 9.6562735184356683e+00 9.3635243482716728e+00 1.3817214020043478e+00 0 0 0
33 1 1.0700092384318864e+01 1.8703247149802406e-02 5.3764748467288328e+00 -1 0 0
34 2 1.0698092821152924e+01 2.7275451171938538e+00 8.1887846771042252e+00 -1 0 0
35 3 2.5595904516932046e+00 2.8221607687054950e-02 8.0670603963325540e+00 0 0 0
36 4 2.8214419517898661e+00 2.8818837322808726e+00 5.4423884446264195e+00 0 0 0
37 5 1.3722461913183779e+00 1.3952374879780634e+00 6.8409604473096373e+00 0 0 0
38 6 1.4876249878676027e+00 4.0821710907970186e+00 9.4410230254944292e+00 0 0 0
39 7 3.9110806914297074e+00 1.3781808590946862e+00 9.6856988043922243e+00 0 0 0
40 8 3.9440249581294013e+00 4.1879712808554626e+00 6.9093173377591039e+00 0 0 0
41 1 5.5141663269005559e+00 1.7645621764308600e-01 5.5306499273458725e+00 0 0 0
42 2 5.5985780491752450e+00 2.7997724883389998e+00 8.1142115135675805e+00 0 0 0
43 3 8.0688992871690530e+00 1.6481945028752995e-01 8.2670009825157464e+00 0 0 0
44 4 8.0871061461850093e+00 2.8829989314598494e+00 5.3855410456855504e+00 0 0 0
45 5 6.9864811057959368e+00 1.4244451123004291e+00 6.9335024333115447e+00 0 0 0
46 6 6.7189272164787059e+00 4.1617273576112819e+00 9.3431993728237934e+00 0 0 0
47 7 9.3396936544866520e+00 1.2592509571339474e+00 9.6308365502537168e+00 0 0 0
48 8 9.3844506274835222e+00 4.2051961155365900e+00 6.8071138234708295e+00 0 0 0
49 1 1.7248042280435583e-01 5.5094660728082365e+00 5.4102856880367201e+00 0 0 0
50 2 3.7450733705167986e-02 7.9809813827585803e+00 8.2751000234673722e+00 0 0 0
51 3 2.7655331604154934e+00 5.5383271031991237e+00 7.9931234676757006e+00 0 0 0
52 4 2.5155467702746610e+00 8.3325680062258929e+00 5.4759806385883039e+00 0 0 0
53 5 1.1807952451962258e+00 6.7101860129653650e+00 6.7638199088792641e+00 0 0 0
54 6 1.1959471910773762e+00 9.6844404374641329e+00 9.5649324596695067e+00 0 0 0
55 7 4.1090326500366361e+00 6.9877491657431232e+00 9.6832286446741698e+00 0 0 0
56 8 4.0458419253065214e+00 9.6567386267038486e+00 6.8650990115647899e+00 0 0 0
57 1 5.4797685959081948e+00 5.4847914290343374e+00 5.5035477801042365e+00 0 0 0
58 2 5.2795203845652381e+00 8.2286033879565554e+00 8.0581413858307709e+00 0 0 0
59 3 8.0498475764577027e+00 5.3937175246191762e+00 8.3399362744881937e+00 0 0 0
60 4 8.3304289868175641e+00 8.2409814428195727e+00 5.3806094685744537e+00 0 0 0
61 5 6.9330690971130133e+00 6.7598151784069209e+00 6.8812034851184363e+00 0 0 0
62 6 6.9458643451878403e+00 9.3250495720304549e+00 9.6826571158517201e+00 0 0 0
63 7 9.3283809458502258e+00 6.9575569047261068e+00 9.4418977316662893e+00 0 0 0
64 8 9.4282304328065276e+00 9.4433841793067455e+00 6.6169016084578596e+00 0 0 0
Velocities
1 -7.6695811444905315e-01 8.8776500375415912e-01 -4.6748679865524317e-01
2 -4.2174334498042004e-01 2.6596349461961127e-01 -1.1334804338647457e+00
3 3.1092663150899669e+00 -3.2607896569135373e+00 -4.5472992935642453e-01
4 -1.0033967676892164e+00 -4.0701495139485546e+00 3.0519108521711837e+00
5 2.1876978647560312e+00 -1.8528542484907762e+00 5.5868611584263783e-01
6 -5.8915345282488856e+00 -1.2670766284310366e+00 -1.4548236578657073e-01
7 -7.4671607451840827e-01 -2.3224748454458921e+00 2.9040191974877243e+00
8 8.8344717384787486e-01 2.1131388234004187e+00 -2.6319923612777498e+00
9 -1.4945940737308610e+00 2.4036759792415352e+00 2.9873898113274451e+00
10 -2.3062527275180000e-02 6.3069649849804210e-01 -4.6199114681815372e+00
11 3.8719801571165269e-01 -2.6757201256087666e+00 -2.8351493398548979e+00
12 3.1622414879535530e+00 1.1788951785955282e-01 -1.6811026088924106e+00
13 -4.9777200700829107e+00 1.0067220620999075e-01 -1.1749631996478570e-01
14 1.6098573779552736e+00 -1.4257777445753939e+00 9.3729752744584949e-01
15 -1.9671428383911080e-01 -1.1467725283686230e+00 -7.1090487650568090e-01
16 2.4293095169865944e+00 -2.2853507053089284e+00 3.6552591604907518e+00
17 2.1486682069514684e-01 6.5398679889262946e-03 -7.8674906209013318e-01
18 -5.9695750825985816e-01 -3.8903164843963536e+00 7.0106707544958913e-01
19 1.8513305622305032e+00 2.7457421924307135e+00 -2.6843196517815027e-01
20 4.6472920038025278e-02 3.3363247063995392e+00 -7.5654131995610463e-01
21 2.0461345318527768e+00 6.5187960424485167e+00 2.2781592760522332e-01
22 -3.2896669679401891e-01 -4.6935568644796639e+00 2.6343294291762615e-01
23 -2.0431037382403300e-01 -1.1908279321425959e+00 -2.1024589473753172e+00
24 -6.1675703823018013e+00 3.7268908602022122e+00 2.2946207883205223e+00
25 9.8131185739798532e-01 1.0773612880108889e-01 1.7659001559413789e+00
26 2.5123700267960087e+00 -9.7029098941340775e-01 -3.7611190518657027e+00
27 -2.8065233782242118e+00 2.7735023884863090e+00 -5.7440441416815013e-01
28 -2.8351435666922815e+00 -2.4736491871242201e+00 -2.7770228999188280e+00
29 -6.1233333948487512e-01 -1.4612515482031314e+00 -2.1246997373192005e+00
30 -1.6587500360685015e+00 1.2439126820981170e+00 4.6333319512528819e+00
31 -1.6739126871847136e+00 -4.0135139175283019e+00 2.4388454178990426e+00
32 -1.1634332347436640e+00 -7.7629078403429219e-01 1.2067789175483656e+00
33 2.8857524470408986e+00 -1.7030276362003458e+00 -2.0845880086526334e+00
34 3.6831626165197040e+00 -3.5993774010234549e-02 -8.0961124509532045e-01
35 -2.8770388338755111e+00 3.9112196797609061e-01 -2.6842134469568530e+00
36 2.3476192919341012e+00 -1.4869539504293825e+00 2.6805229608818411e+00
37 -1.9857985903088504e+00 3.6532965667626152e+00 7.6783019003634334e-01
38 -8.6498749460025504e-05 -1.2786473611543103e+00 -2.5574004902042100e+00
39 3.2183147762059252e+00 2.1412145724457892e+00 -1.3379757716793121e+00
40 -3.3194222393529000e+00 8.6217442393646981e-01 -9.7775722554209368e-02
41 -2.4363036081885721e+00 -2.5050089095178842e+00 -1.7152684549177144e+00
42 -1.8123025300125442e+00 4.1040607170758863e+00 1.8113434768789887e+00
43 8.2116299357978972e-01 -1.4091949665194181e+00 1.5546533259848685e+00
44 -1.5106466229056412e+00 -3.7176405569288479e-01 2.9687407194461857e+00
45 2.0036640890479163e+00 3.4558719013661352e+00 2.4761488653104236e+00
46 1.1557532358053453e-05 6.8233360706012713e-02 -8.1988351060085085e-01
47 2.0610372874209806e+00 2.9250619947397714e+00 -4.6246198532284426e+00
48 3.7769045376898491e+00 -6.2124369701718694e+00 6.5274567582735055e-01
49 4.6074991208714851e+00 8.2503257645594730e-01 8.5565348020904775e-01
50 8.5045797019446467e-01 1.5642419476572114e+00 3.4414259937041352e+00
51 3.0951672150001852e+00 6.4364948036249203e-01 -2.5200572359688507e+00
52 -3.4329134343428513e-01 -3.5864072102511093e+00 -1.3092330149470974e+00
53 -4.3836593017980983e+00 -3.3032188251492345e-01 -4.2201800726103427e+00
54 1.0067907201962536e+00 3.3833856103070516e+00 -4.2244492140600592e-01
55 1.3872579123070348e+00 8.7826766277411539e-01 -9.4887528280134281e-01
56 6.9357081915378493e-01 3.8110270186753179e+00 1.4629354931293179e-01
57 6.6962746178223931e-01 6.6943282268523383e+00 9.9362589535207779e-01
58 -1.7296381154890770e+00 -5.5052794989092768e-01 2.7151993562471821e+00
59 1.1683811118902456e+00 -5.6097747254105945e+00 -1.3465121907588353e+00
60 4.2289642990542493e+00 -5.3831728480380980e-01 3.0410178504652357e+00
61 8.1393552020156468e-01 -8.8749030091659420e-01 2.4504472860529236e+00
62 -2.4947166250287984e+00 2.8424666276480779e+00 1.1665977930274425e+00
63 -8.7979164195267434e-01 2.3389132899677176e+00 3.8359678050967816e-01
64 -3.3977492794459896e+00 -1.2790636562498856e+00 -2.8439591835333616e-01

39
examples/PACKAGES/pod/test/in.test Normal file
View File

@ -0,0 +1,39 @@
variable newton_pair index on
variable newton_bond index on
variable units index metal
variable input_dir index .
variable data_file index ${input_dir}/data.manybody
variable pair_style index 'zero 8.0'
atom_style atomic
atom_modify map array
neigh_modify delay 2 every 2 check no
units ${units}
timestep 0.0001
newton ${newton_pair} ${newton_bond}
pair_style ${pair_style}
read_data ${data_file}
mass 1 180.88
pair_style pod
pair_coeff * * Ta_param.pod Ta_coeff.pod Ta Ta Ta Ta Ta Ta Ta Ta
# Setup output
thermo 1
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run 10

114
potentials/Ta_coeff.pod
View File

@ -1,63 +1,63 @@
POD_coefficients: 62
-3.495093
-59.701906
30.663456
10.791538
0.840297
0.730228
0.910582
-67.196938
-179.985939
524.691284
670.837805
-259.035435
3.823252
52.397945
-63.764311
-120.411099
39.425094
1.642051
-10.593072
0.363492
16.232118
-2.165456
0.014326
0.691317
1.208074
-1.186301
-0.656701
model_coefficients: 62 0 0
-3.495092
-59.702301
30.663465
10.791500
0.840322
0.730233
0.910588
-67.197190
-179.980716
524.692031
670.830056
-259.034640
3.823282
52.396979
-63.764340
-120.409556
39.425007
1.642041
-10.592947
0.363512
16.231934
-2.165453
0.014335
0.691299
1.208040
-1.186298
-0.656703
0.011029
-0.044294
-0.042611
0.025912
0.025913
-0.035474
-5.179647
428.614009
-16.386364
126.893554
-410.027777
-953.238514
-18.330799
1.006988
-22.929962
-0.914978
-4.986332
29.072433
31.345932
0.723031
0.249736
-1.438448
-0.632864
0.148064
2.642487
-0.405224
0.104130
0.107113
-0.020909
-0.498780
0.247484
-5.168418
428.615879
-16.436190
126.897483
-410.022376
-953.258765
-18.282630
1.006650
-22.930080
-0.913472
-4.986589
29.072094
31.347224
0.721552
0.249755
-1.438459
-0.632951
0.148047
2.642466
-0.405122
0.104219
0.107115
-0.020907
-0.498791
0.247485
0.093056
-0.271642
0.355028
1.479538
-0.271639
0.355044
1.479539
-0.216955

2
src/KOKKOS/pair_pod_kokkos.cpp
View File

@ -140,7 +140,7 @@ double PairPODKokkos<DeviceType>::init_one(int i, int j)
template<class DeviceType>
void PairPODKokkos<DeviceType>::coeff(int narg, char **arg)
{
if (narg < 7) utils::missing_cmd_args(FLERR, "pair_coeff", error);
if (narg < 5) utils::missing_cmd_args(FLERR, "pair_coeff", error);
PairPOD::coeff(narg,arg); // create a PairPOD object

13
src/ML-POD/compute_pod_atom.cpp
View File

@ -36,23 +36,18 @@ ComputePODAtom::ComputePODAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), list(nullptr), map(nullptr), pod(nullptr), elements(nullptr)
{
int nargmin = 7;
int nargmin = 6;
if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style);
if (comm->nprocs > 1) error->all(FLERR, "compute command does not support multi processors");
std::string pod_file = std::string(arg[3]); // pod input file
std::string coeff_file = ""; // coefficient input file
std::string proj_file = std::string(arg[4]); // coefficient input file
std::string centroid_file = std::string(arg[5]); // coefficient input file
podptr = new EAPOD(lmp, pod_file, coeff_file, proj_file, centroid_file);
std::string coeff_file = std::string(arg[4]); // coefficient input file
podptr = new EAPOD(lmp, pod_file, coeff_file);
int ntypes = atom->ntypes;
memory->create(map, ntypes + 1, "compute_pod_global:map");
map_element2type(narg - 6, arg + 6, podptr->nelements);
//size_array_rows = 1 + 3*atom->natoms;
//size_array_cols = podptr->nCoeffAll;
map_element2type(narg - 5, arg + 5, podptr->nelements);
cutmax = podptr->rcut;

10
src/ML-POD/compute_pod_global.cpp
View File

@ -38,20 +38,18 @@ ComputePODGlobal::ComputePODGlobal(LAMMPS *lmp, int narg, char **arg) :
array_flag = 1;
extarray = 0;
int nargmin = 7;
int nargmin = 6;
if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style);
if (comm->nprocs > 1) error->all(FLERR, "compute command does not support multi processors");
std::string pod_file = std::string(arg[3]); // pod input file
std::string coeff_file = ""; // coefficient input file
std::string proj_file = std::string(arg[4]); // coefficient input file
std::string centroid_file = std::string(arg[5]); // coefficient input file
podptr = new EAPOD(lmp, pod_file, coeff_file, proj_file, centroid_file);
std::string coeff_file = std::string(arg[4]); // coefficient input file
podptr = new EAPOD(lmp, pod_file, coeff_file);
int ntypes = atom->ntypes;
memory->create(map, ntypes + 1, "compute_pod_global:map");
map_element2type(narg - 6, arg + 6, podptr->nelements);
map_element2type(narg - 5, arg + 5, podptr->nelements);
size_array_rows = 1 + 3*atom->natoms;
size_array_cols = podptr->nCoeffAll;

10
src/ML-POD/compute_pod_local.cpp
View File

@ -38,21 +38,19 @@ ComputePODLocal::ComputePODLocal(LAMMPS *lmp, int narg, char **arg) :
array_flag = 1;
extarray = 0;
int nargmin = 7;
int nargmin = 6;
if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style);
if (comm->nprocs > 1) error->all(FLERR, "compute command does not support multi processors");
std::string pod_file = std::string(arg[3]); // pod input file
std::string coeff_file = ""; // coefficient input file
std::string proj_file = std::string(arg[4]); // coefficient input file
std::string centroid_file = std::string(arg[5]); // coefficient input file
podptr = new EAPOD(lmp, pod_file, coeff_file, proj_file, centroid_file);
std::string coeff_file = std::string(arg[4]); // coefficient input file
podptr = new EAPOD(lmp, pod_file, coeff_file);
int ntypes = atom->ntypes;
memory->create(map, ntypes + 1, "compute_pod_local:map");
map_element2type(narg - 6, arg + 6, podptr->nelements);
map_element2type(narg - 5, arg + 5, podptr->nelements);
int numdesc = podptr->Mdesc * podptr->nClusters;
size_array_rows = 1 + 3*atom->natoms;

10
src/ML-POD/compute_podd_atom.cpp
View File

@ -36,20 +36,18 @@ ComputePODDAtom::ComputePODDAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), list(nullptr), map(nullptr), pod(nullptr), elements(nullptr)
{
int nargmin = 7;
int nargmin = 6;
if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style);
if (comm->nprocs > 1) error->all(FLERR, "compute command does not support multi processors");
std::string pod_file = std::string(arg[3]); // pod input file
std::string coeff_file = ""; // coefficient input file
std::string proj_file = std::string(arg[4]); // coefficient input file
std::string centroid_file = std::string(arg[5]); // coefficient input file
podptr = new EAPOD(lmp, pod_file, coeff_file, proj_file, centroid_file);
std::string coeff_file = std::string(arg[4]); // coefficient input file
podptr = new EAPOD(lmp, pod_file, coeff_file);
int ntypes = atom->ntypes;
memory->create(map, ntypes + 1, "compute_pod_global:map");
map_element2type(narg - 6, arg + 6, podptr->nelements);
map_element2type(narg - 5, arg + 5, podptr->nelements);
cutmax = podptr->rcut;

196
src/ML-POD/eapod.cpp
View File

@ -37,7 +37,7 @@ using MathSpecial::powint;
#define MAXLINE 1024
// constructor
EAPOD::EAPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff_file, const std::string &proj_file, const std::string &centroids_file) :
EAPOD::EAPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff_file) :
Pointers(_lmp), elemindex(nullptr), Phi(nullptr), Lambda(nullptr), Proj(nullptr),
Centroids(nullptr), bd(nullptr), bdd(nullptr), pd(nullptr), pdd(nullptr), coeff(nullptr), tmpmem(nullptr), tmpint(nullptr),
pn3(nullptr), pq3(nullptr), pc3(nullptr), pq4(nullptr), pa4(nullptr), pb4(nullptr), pc4(nullptr),
@ -94,27 +94,31 @@ EAPOD::EAPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff
// read pod input file to podstruct
read_pod_file(pod_file);
// read pod coefficient file to podstruct
if (coeff_file != "") {
ncoeff = read_coeff_file(coeff_file);
if (ncoeff != nCoeffAll)
error->all(FLERR,"number of coefficients in the coefficient file is not correct");
}
if (nClusters > 1) {
// read projection matrix file to podstruct
if (proj_file != "") {
nproj = read_projection_matrix(proj_file);
if (nproj != nComponents*Mdesc*nelements)
error->all(FLERR,"number of coefficients in the projection file is not correct");
read_model_coeff_file(coeff_file);
}
// read centroids file to podstruct
if (centroids_file != "") {
ncentroids = read_centroids(centroids_file);
if (ncentroids != nComponents*nClusters*nelements)
error->all(FLERR,"number of coefficients in the projection file is not correct");
}
}
// // read pod coefficient file to podstruct
// if (coeff_file != "") {
// ncoeff = read_coeff_file(coeff_file);
// if (ncoeff != nCoeffAll)
// error->all(FLERR,"number of coefficients in the coefficient file is not correct");
// }
// if (nClusters > 1) {
// // read projection matrix file to podstruct
// if (proj_file != "") {
// nproj = read_projection_matrix(proj_file);
// if (nproj != nComponents*Mdesc*nelements)
// error->all(FLERR,"number of coefficients in the projection file is not correct");
// }
// // read centroids file to podstruct
// if (centroids_file != "") {
// ncentroids = read_centroids(centroids_file);
// if (ncentroids != nComponents*nClusters*nelements)
// error->all(FLERR,"number of coefficients in the projection file is not correct");
// }
// }
}
// destructor
@ -422,6 +426,157 @@ void EAPOD::read_pod_file(std::string pod_file)
}
}
void EAPOD::read_model_coeff_file(std::string coeff_file)
{
std::string coefffilename = coeff_file;
FILE *fpcoeff;
if (comm->me == 0) {
fpcoeff = utils::open_potential(coefffilename,lmp,nullptr);
if (fpcoeff == nullptr)
error->one(FLERR,"Cannot open model coefficient file {}: ", coefffilename, utils::getsyserror());
}
// check format for first line of file
char line[MAXLINE],*ptr;
int eof = 0;
int nwords = 0;
while (nwords == 0) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == nullptr) {
eof = 1;
fclose(fpcoeff);
}
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
// strip comment, skip line if blank
nwords = utils::count_words(utils::trim_comment(line));
}
if (nwords != 4)
error->all(FLERR,"Incorrect format in POD coefficient file");
// strip single and double quotes from words
int ncoeffall, nprojall, ncentall;
std::string tmp_str;
try {
ValueTokenizer words(utils::trim_comment(line),"\"' \t\n\r\f");
tmp_str = words.next_string();
ncoeffall = words.next_int();
nprojall = words.next_int();
ncentall = words.next_int();
} catch (TokenizerException &e) {
error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what());
}
// loop over single block of coefficients and insert values in coeff
memory->create(coeff, ncoeffall, "pod:pod_coeff");
for (int icoeff = 0; icoeff < ncoeffall; icoeff++) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == nullptr) {
eof = 1;
fclose(fpcoeff);
}
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) error->all(FLERR,"Incorrect format in model coefficient file");
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
try {
ValueTokenizer cff(utils::trim_comment(line));
if (cff.count() != 1) error->all(FLERR,"Incorrect format in model coefficient file");
coeff[icoeff] = cff.next_double();
} catch (TokenizerException &e) {
error->all(FLERR,"Incorrect format in model coefficient file: {}", e.what());
}
}
memory->create(Proj, nprojall, "pod:pca_proj");
for (int iproj = 0; iproj < nprojall; iproj++) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == nullptr) {
eof = 1;
fclose(fpcoeff);
}
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) error->all(FLERR,"Incorrect format in model coefficient file");
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
try {
ValueTokenizer cff(utils::trim_comment(line));
if (cff.count() != 1) error->all(FLERR,"Incorrect format in model coefficient file");
Proj[iproj] = cff.next_double();
} catch (TokenizerException &e) {
error->all(FLERR,"Incorrect format in model coefficient file: {}", e.what());
}
}
memory->create(Centroids, ncentall, "pod:pca_cent");
for (int icent = 0; icent < ncentall; icent++) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == nullptr) {
eof = 1;
fclose(fpcoeff);
}
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) error->all(FLERR,"Incorrect format in model coefficient file");
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
try {
ValueTokenizer cff(utils::trim_comment(line));
if (cff.count() != 1) error->all(FLERR,"Incorrect format in model coefficient file");
Centroids[icent] = cff.next_double();
} catch (TokenizerException &e) {
error->all(FLERR,"Incorrect format in model coefficient file: {}", e.what());
}
}
if (comm->me == 0) {
if (!eof) fclose(fpcoeff);
}
if (ncoeffall != nCoeffAll)
error->all(FLERR,"number of coefficients in the coefficient file is not correct");
if (nClusters > 1) {
if (nprojall != nComponents*Mdesc*nelements)
error->all(FLERR,"number of coefficients in the projection file is not correct");
if (ncentall != nComponents*nClusters*nelements)
error->all(FLERR,"number of coefficients in the projection file is not correct");
}
if (comm->me == 0) {
utils::logmesg(lmp, "**************** Begin of Model Coefficients ****************\n");
utils::logmesg(lmp, "total number of coefficients for POD potential: {}\n", ncoeffall);
utils::logmesg(lmp, "total number of elements for PCA projection matrix: {}\n", nprojall);
utils::logmesg(lmp, "total number of elements for PCA centroids: {}\n", ncentall);
utils::logmesg(lmp, "**************** End of Model Coefficients ****************\n\n");
}
}
int EAPOD::read_coeff_file(std::string coeff_file)
{
std::string coefffilename = coeff_file;
@ -499,6 +654,7 @@ int EAPOD::read_coeff_file(std::string coeff_file)
error->all(FLERR,"Incorrect format in POD coefficient file: {}", e.what());
}
}
if (comm->me == 0) {
if (!eof) fclose(fpcoeff);
}
@ -506,7 +662,7 @@ int EAPOD::read_coeff_file(std::string coeff_file)
if (comm->me == 0) {
utils::logmesg(lmp, "**************** Begin of POD Coefficients ****************\n");
utils::logmesg(lmp, "total number of coefficients for POD potential: {}\n", ncoeffall);
utils::logmesg(lmp, "**************** End of POD Potentials ****************\n\n");
utils::logmesg(lmp, "**************** End of POD Coefficients ****************\n\n");
}
return ncoeffall;

3
src/ML-POD/eapod.h
View File

@ -154,7 +154,7 @@ public:
int nld33, nld34, nld44, ngd33, ngd34, ngd44;
int *ind33l, *ind33r, *ind34l, *ind34r, *ind44l, *ind44r;
EAPOD(LAMMPS *, const std::string &pod_file, const std::string &coeff_file, const std::string &proj_file, const std::string &centroids_file);
EAPOD(LAMMPS *, const std::string &pod_file, const std::string &coeff_file);
EAPOD(LAMMPS *lmp) : Pointers(lmp){};
~EAPOD() override;
@ -163,6 +163,7 @@ public:
void print_matrix(const char* desc, int m, int n, double* a, int lda );
void read_pod_file(std::string pod_file);
void read_model_coeff_file(std::string coeff_file);
int read_coeff_file(std::string coeff_file);
int read_projection_matrix(std::string proj_file);
int read_centroids(std::string centroids_file);

66
src/ML-POD/fitpod_command.cpp
View File

@ -56,16 +56,8 @@ void FitPOD::command(int narg, char **arg)
coeff_file = std::string(arg[2]); // coefficient input file
else
coeff_file = "";
if (narg > 3)
proj_file = std::string(arg[3]); // projection input file
else
proj_file = "";
if (narg > 4)
cent_file = std::string(arg[4]); // centroid input file
else
cent_file = "";
fastpodptr = new EAPOD(lmp, pod_file, coeff_file, proj_file, cent_file);
fastpodptr = new EAPOD(lmp, pod_file, coeff_file);
desc.nCoeffAll = fastpodptr->nCoeffAll;
desc.nClusters = fastpodptr->nClusters;
@ -97,9 +89,33 @@ void FitPOD::command(int narg, char **arg)
}
// compute POD coefficients using least-squares method
if (coeff_file == "") {
least_squares_fit(traindata);
if (coeff_file == "") least_squares_fit(traindata);
//error->all(FLERR, "stop after least_squares_fit");
if (comm->me == 0) { // save coefficients into a text file
std::string filename = traindata.filenametag + "_coefficients" + ".pod";
FILE *fp = fopen(filename.c_str(), "w");
int nCoeffAll = desc.nCoeffAll;
int n1 = 0, n2=0;
if (((int) envdata.data_path.size() > 1) && (desc.nClusters > 1)) {
n1 = fastpodptr->nComponents*fastpodptr->Mdesc*fastpodptr->nelements;
n2 = fastpodptr->nComponents*fastpodptr->nClusters*fastpodptr->nelements;
}
fmt::print(fp, "model_coefficients: {} {} {}\n", nCoeffAll, n1, n2);
for (int count = 0; count < nCoeffAll; count++) {
fmt::print(fp, "{:<10.{}f}\n", desc.c[count], traindata.precision);
}
for (int count = 0; count < n1; count++) {
fmt::print(fp, "{:<10.{}f}\n", fastpodptr->Proj[count], 14);
}
for (int count = 0; count < n2; count++) {
fmt::print(fp, "{:<10.{}f}\n", fastpodptr->Centroids[count], 14);
}
fclose(fp);
}
}
// calculate errors for the training data set
@ -1464,10 +1480,10 @@ void FitPOD::environment_cluster_calculation(const datastruct &data)
MPI_Barrier(MPI_COMM_WORLD);
}
if (comm->me == 0) {
savedata2textfile(data.filenametag + "_projection_matrix" + ".pod", "projection_matrix: {}\n ", fastpodptr->Proj, nComponents*Mdesc*nelements, 1, 1);
savedata2textfile(data.filenametag + "_centroids" + ".pod", "centroids: {} \n", fastpodptr->Centroids, nComponents*nClusters*nelements, 1, 1);
}
// if (comm->me == 0) {
// savedata2textfile(data.filenametag + "_projection_matrix" + ".pod", "projection_matrix: {}\n ", fastpodptr->Proj, nComponents*Mdesc*nelements, 1, 1);
// savedata2textfile(data.filenametag + "_centroids" + ".pod", "centroids: {} \n", fastpodptr->Centroids, nComponents*nClusters*nelements, 1, 1);
// }
memory->destroy(basedescmatrix);
memory->destroy(pca);
@ -1615,17 +1631,17 @@ void FitPOD::least_squares_fit(const datastruct &data)
// update coefficients in POD class to compute energy and force
fastpodptr->mknewcoeff(desc.c, nCoeffAll);
if (comm->me == 0) { // save coefficients into a text file
std::string filename = data.filenametag + "_coefficients" + ".pod";
FILE *fp = fopen(filename.c_str(), "w");
// if (comm->me == 0) { // save coefficients into a text file
// std::string filename = data.filenametag + "_coefficients" + ".pod";
// FILE *fp = fopen(filename.c_str(), "w");
fmt::print(fp, "POD_coefficients: {}\n", nCoeffAll);
for (int count = 0; count < nCoeffAll; count++) {
fmt::print(fp, "{:<10.{}f}\n", desc.c[count], data.precision);
}
fclose(fp);
utils::logmesg(lmp, "**************** End of Least-Squares Fitting ****************\n");
}
// fmt::print(fp, "POD_coefficients: {}\n", nCoeffAll);
// for (int count = 0; count < nCoeffAll; count++) {
// fmt::print(fp, "{:<10.{}f}\n", desc.c[count], data.precision);
// }
// fclose(fp);
// utils::logmesg(lmp, "**************** End of Least-Squares Fitting ****************\n");
// }
}
double latticevolume(double *lattice)

13
src/ML-POD/pair_pod.cpp
View File

@ -290,21 +290,14 @@ void PairPOD::coeff(int narg, char **arg)
map = new int[np1];
allocated = 1;
if (narg < 7) utils::missing_cmd_args(FLERR, "pair_coeff", error);
if (narg < 5) utils::missing_cmd_args(FLERR, "pair_coeff", error);
std::string pod_file = std::string(arg[2]); // pod input file
std::string coeff_file = std::string(arg[3]); // coefficient input file
std::string proj_file = std::string(arg[4]); // projection matrix file
std::string centroid_file = std::string(arg[5]); // centroid matrix file
map_element2type(narg - 6, arg + 6);
map_element2type(narg - 4, arg + 4);
delete fastpodptr;
fastpodptr = new EAPOD(lmp, pod_file, coeff_file, proj_file, centroid_file);
if (fastpodptr->nClusters > 1) {
if (proj_file == "") error->all(FLERR,"The projection file name can not be empty when the number of clusters is greater than 1.");
if (centroid_file == "") error->all(FLERR,"The centroids file name can not be empty when the number of clusters is greater than 1.");
}
fastpodptr = new EAPOD(lmp, pod_file, coeff_file);
copy_data_from_pod_class();
rcut = fastpodptr->rcut;