-
Notifications
You must be signed in to change notification settings - Fork 2
/
README.txt
227 lines (174 loc) · 9.36 KB
/
README.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
-----------------------------------------------------------------------
04-26-2019
ALADYN_PI mini-app is a simple molecular dynamics (MD) code for performing
constant energy atomistic simulations using either a straight
Artificial Neural Network (ANN) interatomic potential, or
Physically Informed Neural Network (PINN) interatomic potential.
References:
1. Vesselin I. Yamakov, Edward H. Glaessgen, NASA/TM-2019-220431
(https://ntrs.nasa.gov/citations/20200000069)
2. G.P.Purja Pun, V.Yamakov, J.Hickman, E.H.Glaessgen, Y.Mishin,
Physical Review Materials, 4, 113807 (2020).
(https://link.aps.org/doi/10.1103/PhysRevMaterials.4.113807)
The trained ANN was produced and offered by Ganga P. Pun and Yuri Mishin
from George Mason University.
=======================================================================
COMPILATION
-----------------------------------------------------------------------
* FORTRAN compiler (Intel 2003 or newer, or PGI FORTRAN with OpenACC)
-----------------------------------------------------------------------
Source directory: ALADYN_PI.source
-----------------------------------------------------------------------
Compilation: use the provided makefiles with the following options:
Intel compiler:
> make -f makefile.intel ! compiles with -O3 optimization on
> make -f makefile.intel DEBUG=TRUE ! check and warning flags on
> make -f makefile.intel OMP=TRUE ! compile with OpenMP direectives
PGI compiler:
> make -f makefile.pgi ! compiles with -O3 optimization on
> make -f makefile.pgi DEBUG=TRUE ! check and warning flags on
> make -f makefile.pgi OMP=TRUE ! compile with OpenMP direectives
> make -f makefile.pgi ACC=TRUE ! compile with OpenMP+OpenACC direectives
Edit the provided makefiles for specific compiler option of your choice
=======================================================================
EXECUTION
-----------------------------------------------------------------------
Run from the example (test) directory: ALADYN_PI.test
Running a tets case:
> aladyn_pi ! executes 10 MD steps report at each step
> aladyn_pi -n 100 -m 10 ! executes 100 MD steps, report at each 10-th step
Available PBS scripts used for NASA/LaRC K3 cluster:
ALADYN_PI_intel.job - run the intel version
ALADYN_PI_pgi_V100.job - run the pgi version with OpneACC for V100 gpu.
Screen output is riderected to aladyn_pi.out
Example outputs are saved in: aladyn_pi_intel.out and aladyn_pi_pgi.out
=======================================================================
INPUT FILES:
-----------------------------------------------------------------------
PINN.dat - Neural network potential file
structure.plt - input atomic structure file
-----------------------------------------------------------------------
--- Available potential files in directory POT:
(to be linked or copied as PINN.dat in the working directory of aladyn_pi)
ANN_Si.dat - Straight Artificial Neural Network potential for Si
PINN_Si.dat - Physically Informed Neural Network potential for Si
PINN_Al.dat - Physically Informed Neural Network potential for Al (ref.2)
-----------------------------------------------------------------------
--- Available Si single crystal test structures in directory STR_Si:
Si_N4000.plt - 4000 atoms Si crystal
Si_N8000.plt - 8000 atoms Si crystal
Si_N16000.plt - 16000 atoms Si crystal
Si_N32000.plt - 32000 atoms Si crystal
Si_N64000.plt - 64000 atoms Si crystal
Si_N128000.plt - 128000 atoms Si crystal
Si_N192000.plt - 192000 atoms Si crystal
Si_N256000.plt - 256000 atoms Si crystal
Si_N512000.plt - 512000 atoms Si crystal
-----------------------------------------------------------------------
--- Available Al single crystal test structures in directory STR_Al:
Al_N4000.plt - 4000 atoms Al crystal
Al_N8000.plt - 8000 atoms Al crystal
Al_N16000.plt - 16000 atoms Al crystal
Al_N32000.plt - 32000 atoms Al crystal
Al_N64000.plt - 64000 atoms Al crystal
Al_N128000.plt - 128000 atoms Al crystal
Al_N192000.plt - 192000 atoms Al crystal
Al_N256000.plt - 256000 atoms Al crystal
Use any of the above structures by linking them to structure.plt, e.g.,
> ln -s STR/Al_N4000.plt structure.plt
=======================================================================
SOURCE FILES:
File: ALADYN_PI.source.zip contains Full Double PRECISION ANN calculation and BOP calculations.
File: ALADYN_PIs.source.zip contains SINGLE PRECISION ( rela(kind=4) ) ANN calculation and Double PRECISION BOP calculations.
-----------------------
Files in ALADYN_PI.source.zip
aladyn_pi.f - Main program
aladyn_pi_sys.f - system modul
aladyn_pi_sys_OMP.f - system modul for OpneMP compilation
aladyn_pi_sys_NO_OMP.f - system modul without OpneMP compilation
aladyn_pi_sys_ACC.f - system modul for OpneACC compilation
aladyn_pi_mods.f - contains general purpose modules
aladyn_pi_IO.f - I/O operations
aladyn_pi_ANN_OMP.f - Artificial Neural Network OpneMP code
contains:
subroutine Frc_ANN_OMP ! ANN force & energy (OpenMP version)
aladyn_pi_ANN_ACC.f - Artificial Neural Network OpneACC code
subroutine Frc_ANN_ACC ! ANN force & energy (OpenACC version)
aladyn_pi_PINN_OMP.f - Physically Informed NN OpneMP code
subroutine Frc_PINN_OMP ! PINN force & energy (OpenMP version)
aladyn_pi_PINN_ACC.f - Physically Informed NN OpneACC code
subroutine Frc_PINN_ACC ! PINN force & energy (OpenACC version)
aladyn_pi_MD.f - molecular dynamics module
contains:
subroutine get_T ! Calculates current system temperature
subroutine predict_atoms ! Gear predictor call !
subroutine correct_atoms ! Gear corrector call !
-----------------------
Files in ALADYN_PIs.source.zip
aladyn_pi.f - Main program
aladyn_pi_sys.f - system modul
aladyn_pi_sys_OMP.f - system modul for OpneMP compilation
aladyn_pi_sys_NO_OMP.f - system modul without OpneMP compilation
aladyn_pi_sys_ACC.f - system modul for OpneACC compilation
aladyn_pi_mods.f - contains general purpose modules
aladyn_pi_IO.f - I/O operations
aladyn_pi_ANN_OMPs.f - Single Precision Artificial Neural Network OpneMP code
contains:
subroutine Frc_ANN_OMP ! ANN force & energy (OpenMP version)
aladyn_pi_ANN_ACCs.f - Single Precision Artificial Neural Network OpneACC code
subroutine Frc_ANN_ACC ! ANN force & energy (OpenACC version)
aladyn_pi_PINN_OMP.f - Physically Informed NN OpneMP code
subroutine Frc_PINN_OMP ! PINN force & energy (OpenMP version)
aladyn_pi_PINN_ACC.f - Physically Informed NN OpneACC code
subroutine Frc_PINN_ACC ! PINN force & energy (OpenACC version)
aladyn_pi_MD.f - molecular dynamics module
contains:
subroutine get_T ! Calculates current system temperature
subroutine predict_atoms ! Gear predictor call !
subroutine correct_atoms ! Gear corrector call !
-----------------------------------------------------------------------
Suggested subroutines for optimization:
Frc_ANN_OMP and Frc_ANN_ACC (Optimized versions from ALADYN miniapp)
Frc_PINN_OMP and Frc_PINN_ACC
(Optimized versions from ALADYN miniapp)
-----------------------------------------------------------------------
For further information contact:
Vesselin Yamakov
National Institute of Aerospace
100 Exploration Way,
Hampton, VA 23666
phone: (757)-864-2850
fax: (757)-864-8911
e-mail: yamakov@nianet.org
=======================================================================
Notices:
Copyright 2020 United States Government as represented by the
Administrator of the National Aeronautics and Space Administration.
All Rights Reserved.
Disclaimers:
No Warranty: THE SUBJECT SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY
WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY,
INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SUBJECT SOFTWARE
WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR FREEDOM FROM
INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE ERROR
FREE, OR ANY WARRANTY THAT DOCUMENTATION, IF PROVIDED, WILL CONFORM
TO THE SUBJECT SOFTWARE. THIS AGREEMENT DOES NOT, IN ANY MANNER,
CONSTITUTE AN ENDORSEMENT BY GOVERNMENT AGENCY OR ANY PRIOR RECIPIENT
OF ANY RESULTS, RESULTING DESIGNS, HARDWARE, SOFTWARE PRODUCTS OR ANY
OTHER APPLICATIONS RESULTING FROM USE OF THE SUBJECT SOFTWARE.
FURTHER, GOVERNMENT AGENCY DISCLAIMS ALL WARRANTIES AND LIABILITIES
REGARDING THIRD-PARTY SOFTWARE, IF PRESENT IN THE ORIGINAL SOFTWARE,
AND DISTRIBUTES IT "AS IS."
Waiver and Indemnity:
RECIPIENT AGREES TO WAIVE ANY AND ALL CLAIMS AGAINST THE UNITED STATES
GOVERNMENT, ITS CONTRACTORS AND SUBCONTRACTORS, AS WELL AS ANY PRIOR
RECIPIENT. IF RECIPIENT'S USE OF THE SUBJECT SOFTWARE RESULTS IN ANY
LIABILITIES, DEMANDS, DAMAGES, EXPENSES OR LOSSES ARISING FROM SUCH
USE, INCLUDING ANY DAMAGES FROM PRODUCTS BASED ON, OR RESULTING FROM,
RECIPIENT'S USE OF THE SUBJECT SOFTWARE, RECIPIENT SHALL INDEMNIFY AND
HOLD HARMLESS THE UNITED STATES GOVERNMENT, ITS CONTRACTORS AND
SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT, TO THE EXTENT PERMITTED
BY LAW. RECIPIENT'S SOLE REMEDY FOR ANY SUCH MATTER SHALL BE THE
IMMEDIATE, UNILATERAL TERMINATION OF THIS AGREEMENT.
=======================================================================