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nasa / aladynpi

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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

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."


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