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maybe the last one

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kipbarrett
2021-01-29 17:09:40 -06:00
parent ec82a4602d
commit 908562588e
30 changed files with 471 additions and 1485 deletions
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1
doc/src/Commands_pair.rst
View File

@ -221,6 +221,7 @@ OPT.
* :doc:`polymorphic <pair_polymorphic>`
* :doc:`python <pair_python>`
* :doc:`quip <pair_quip>`
* :doc:`rann <pair_rann>`
* :doc:`reax/c (ko) <pair_reaxc>`
* :doc:`rebo (io) <pair_airebo>`
* :doc:`resquared (go) <pair_resquared>`

4
doc/src/pair_rann.rst
View File

@ -253,7 +253,7 @@ is given by:
E = \sum_{\alpha} E^{\alpha}\\\\
E^{\alpha} = {}^{N}\!A^{\alpha}\\\\
{}^{n+1}\!A_i^{\alpha} = {}^{n}\!F\left({}^{n}\!W_{ij}{\;}^{n}\!A_j^{\alpha}+{}^{n}\!B_i\right)\\\\
{}^{0}\!A_i^{\alpha} = \left[\begin{array} S{}^1\!S\!f^\alpha\\ {}^2\!S\!f^\alpha \\...\\\end{array}\right]
{}^{0}\!A_i^{\alpha} = \left[\begin{array}{c} {}^1\!S\!f^\alpha\\ {}^2\!S\!f^\alpha \\...\\\end{array}\right]
Here :math:`E^\alpha` is the energy of atom :math:`\alpha`, :math:`{}^n\!F()`, :math:`{}^n\!W_{ij}` and :math:`{}^n\!B_i` are
the activation function, weight matrix and bias vector of the n-th layer respectively. The
@ -283,7 +283,7 @@ is the bond angle:
\\
C = \frac{2\left(X^{\alpha\gamma}+X^{\gamma\beta}\right)-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2-1}{1-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2}\\
\\
f_c(x) = \left[\begin{array} 11 \; x \geq 1\\ \left(1-\left(1-x\right)^4\right)^2 \; 0<x<1\\0\;x\leq0\end{array}\right.\\
f_c(x) = \left[\begin{array}{l} 1 \; \: x \geq 1\\ \left(1-\left(1-x\right)^4\right)^2 \; \: 0<x<1\\0\; \; x\leq0\end{array}\right.\\
\\
S^{\alpha\beta\gamma} = f_c\left(\frac{C-C_{min}}{C_{max}-C_{min}}\right)\\
\\

1
doc/src/pair_style.rst
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@ -284,6 +284,7 @@ accelerated styles exist.
* :doc:`polymorphic <pair_polymorphic>` - polymorphic 3-body potential
* :doc:`python <pair_python>` -
* :doc:`quip <pair_quip>` -
* :doc:`rann <pair_rann>` -
* :doc:`reax/c <pair_reaxc>` - ReaxFF potential in C
* :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential

91
potentials/Mg.rann
View File

@ -1,91 +0,0 @@
# Neural Network Potential file created by MATLAB
atomtypes:
Mg
mass:Mg:
24.305
fingerprints:Mg_Mg:
radialpower_0
fingerprints:Mg_Mg_Mg:
bondpower_0
fingerprintconstants:Mg_Mg:radialpower_0:re:
3.1936
fingerprintconstants:Mg_Mg:radialpower_0:rc:
6
fingerprintconstants:Mg_Mg:radialpower_0:dr:
2.8064
fingerprintconstants:Mg_Mg:radialpower_0:n:
3
fingerprintconstants:Mg_Mg:radialpower_0:o:
-1
fingerprintconstants:Mg_Mg:radialpower_0:alpha:
5.52 5.52 5.52 5.52 5.52
fingerprintconstants:Mg_Mg_Mg:bondpower_0:re:
3.1936
fingerprintconstants:Mg_Mg_Mg:bondpower_0:rc:
6
fingerprintconstants:Mg_Mg_Mg:bondpower_0:dr:
2.8064
fingerprintconstants:Mg_Mg_Mg:bondpower_0:m:
8
fingerprintconstants:Mg_Mg_Mg:bondpower_0:alphak:
1 2 6 9
fingerprintconstants:Mg_Mg_Mg:bondpower_0:k:
4
networklayers:Mg:
3
layersize:Mg:0:
37
layersize:Mg:1:
20
layersize:Mg:2:
1
weight:Mg:0:
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bias:Mg:0:
-5.812840455195256
15.010638582099496
29.624659288791705
6.089482003604780
-20.183942564953359
-19.131750622870765
25.425690046060971
27.624111929794111
0.740297410586282
-4.844537022087861
20.211971127789965
-3.950026427133535
28.926886494246766
25.304822365917076
27.383284316546206
-14.878350779530585
-13.726815004417979
0.300936029014161
-1.610552372672948
17.876279610284211
weight:Mg:1:
8.393525190816597 -9.799005074799757 -7.735480085336927 -8.104124576752014 12.240026012539039 5.213425998776577 -3.945232488424331 -5.429176982828405 -99.914578185849578 3.921063641589451 -12.243519026057772 3.482819561249847 -6.785425943665748 -4.818862897620001 -5.773098229238692 5.383347312306200 8.019798211775075 8.499369933136281 3.569846715528147 -8.397559798533649
bias:Mg:1:
1713.7664607023298
activationfunctions:Mg:0:
sigI
activationfunctions:Mg:1:
linear

17
src/activation.cpp
View File

@ -10,10 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "activation.h"

17
src/activation.h
View File

@ -10,10 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifndef ACTIVATION_H_
#define ACTIVATION_H_

20
src/activation_linear.cpp
View File

@ -10,14 +10,26 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include <math.h>
#include "activation_linear.h"
#include "activation.h"
using namespace LAMMPS_NS;

18
src/activation_linear.h
View File

@ -10,11 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
*/
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef ACTIVATION_CLASS
ActivationStyle(linear,Activation_linear)

17
src/activation_sigI.cpp
View File

@ -10,12 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
#include <math.h>
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "activation_sigI.h"
using namespace LAMMPS_NS;

19
src/activation_sigI.h
View File

@ -10,10 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
*/
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef ACTIVATION_CLASS

21
src/fingerprint.cpp
View File

@ -10,18 +10,25 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "fingerprint.h"
#include <math.h>
#include <cmath>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <iostream>
using namespace LAMMPS_NS;

18
src/fingerprint.h
View File

@ -10,10 +10,24 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
----------------*/
#ifndef FINGERPRINT_H_
#define FINGERPRINT_H_

23
src/fingerprint_bond.cpp
View File

@ -10,21 +10,26 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@cavs.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "fingerprint_bond.h"
#include "fingerprint.h"
#include <math.h>
#include <cmath>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <iostream>
using namespace LAMMPS_NS;

17
src/fingerprint_bond.h
View File

@ -10,10 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef FINGERPRINT_CLASS

22
src/fingerprint_bondscreened.cpp
View File

@ -10,21 +10,25 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@cavs.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "fingerprint_bondscreened.h"
#include "fingerprint.h"
#include <math.h>
#include <cmath>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <iostream>
using namespace LAMMPS_NS;

16
src/fingerprint_bondscreened.h
View File

@ -10,11 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef FINGERPRINT_CLASS
FingerprintStyle(bondscreened,Fingerprint_bondscreened)

24
src/fingerprint_bondscreenedspin.cpp
View File

@ -10,21 +10,25 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@cavs.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "fingerprint_bondscreenedspin.h"
#include "fingerprint.h"
#include <math.h>
#include <cmath>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <iostream>
using namespace LAMMPS_NS;

16
src/fingerprint_bondscreenedspin.h
View File

@ -10,11 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef FINGERPRINT_CLASS
FingerprintStyle(bondscreenedspin,Fingerprint_bondscreenedspin)

24
src/fingerprint_bondspin.cpp
View File

@ -10,21 +10,25 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@cavs.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "fingerprint_bondspin.h"
#include "fingerprint.h"
#include <math.h>
#include <cmath>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <iostream>
using namespace LAMMPS_NS;

16
src/fingerprint_bondspin.h
View File

@ -10,11 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef FINGERPRINT_CLASS
FingerprintStyle(bondspin,Fingerprint_bondspin)

24
src/fingerprint_radial.cpp
View File

@ -10,20 +10,26 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "fingerprint_radial.h"
#include "fingerprint.h"
#include <math.h>
#include <cmath>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <iostream>
using namespace LAMMPS_NS;

16
src/fingerprint_radial.h
View File

@ -10,11 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef FINGERPRINT_CLASS
FingerprintStyle(radial,Fingerprint_radial)

23
src/fingerprint_radialscreened.cpp
View File

@ -10,19 +10,26 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "fingerprint_radialscreened.h"
#include <cmath>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <iostream>
using namespace LAMMPS_NS;

16
src/fingerprint_radialscreened.h
View File

@ -10,11 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef FINGERPRINT_CLASS
FingerprintStyle(radialscreened,Fingerprint_radialscreened)

24
src/fingerprint_radialscreenedspin.cpp
View File

@ -10,19 +10,25 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "fingerprint_radialscreenedspin.h"
#include <cmath>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <iostream>
using namespace LAMMPS_NS;

16
src/fingerprint_radialscreenedspin.h
View File

@ -10,11 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef FINGERPRINT_CLASS
FingerprintStyle(radialscreenedspin,Fingerprint_radialscreenedspin)

24
src/fingerprint_radialspin.cpp
View File

@ -10,21 +10,25 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#include "fingerprint_radialspin.h"
#include "fingerprint.h"
#include <math.h>
#include <cmath>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <iostream>
using namespace LAMMPS_NS;

17
src/fingerprint_radialspin.h
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@ -10,10 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Christopher Barrett (MSU) barrett@me.msstate.edu
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef FINGERPRINT_CLASS

1354
src/pair_rann.cpp
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File diff suppressed because it is too large Load Diff

40
src/pair_rann.h
View File

@ -10,12 +10,23 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Christopher Barrett (MSU) barrett@me.msstate.edu
Doyl Dickel (MSU) doyl@cavs.msstate.edu
Doyl Dickel (MSU) doyl@me.msstate.edu
----------------------------------------------------------------------*/
/*
“The research described and the resulting data presented herein, unless
otherwise noted, was funded under PE 0602784A, Project T53 "Military
Engineering Applied Research", Task 002 under Contract No. W56HZV-17-C-0095,
managed by the U.S. Army Combat Capabilities Development Command (CCDC) and
the Engineer Research and Development Center (ERDC). The work described in
this document was conducted at CAVS, MSU. Permission was granted by ERDC
to publish this information. Any opinions, findings and conclusions or
recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the United States Army.​”
DISTRIBUTION A. Approved for public release; distribution unlimited. OPSEC#4918
*/
#ifdef PAIR_CLASS
@ -26,14 +37,26 @@ PairStyle(rann,PairRANN)
#ifndef LMP_PAIR_RANN
#define LMP_PAIR_RANN
#define MAXLINE 4096
#define MAXLINE 1024
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <iostream>
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "update.h"
#include "pair.h"
#include <map>
#include <math.h>
#include <string>
#include <sys/resource.h>
namespace LAMMPS_NS {
@ -49,7 +72,7 @@ class PairRANN : public Pair {
void init_style();
double init_one(int, int);
void init_list(int , NeighList *);
void errorf(char*);
void errorf(const char*);
int count_words(char *);
//black magic for modular fingerprints and activations
class Activation ***activation;
@ -79,8 +102,6 @@ class PairRANN : public Pair {
bool dospin;
int res;//Resolution of function tables for cubic interpolation.
int memguess;
// double *Sik,*dSikx,*dSiky,*dSikz,*dSijkx,*dSijky,*dSijkz;
// bool *Bij;
double *screening_min;
double *screening_max;
bool **weightdefined;
@ -137,11 +158,8 @@ class PairRANN : public Pair {
void propagateforward(double *,double *,double *,double *,double *,double **,double **,int,int,int*);//called by compute to get force and energy
void propagateforwardspin(double *,double *,double *,double *,double *,double *,double *,double *,double **,double **,double**,int,int,int*);//called by compute to get force and energy
void screen(double*,double*,double*,double*,double*,double*,double*,bool*,int,int,double*,double*,double*,int *,int);
void testdfeatures(double *,double *, double *, double *,double *,double *, double *,int);
void testdenergy();
void cull_neighbor_list(double *,double *,double *,int *,int *,int *,int,int);
void screen_neighbor_list(double *,double *,double *,int *,int *,int *,int,int,bool*,double*,double*,double*,double*,double*,double*,double*);
void update_stack_size();
};
}