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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.

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 COMPILATION

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* FORTRAN compiler (Intel 2003 or newer, or PGI FORTRAN with OpenACC)
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Source directory: ALADYN_PI.source
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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
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 EXECUTION

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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
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INPUT FILES:

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PINN.dat - Neural network potential file
structure.plt - input atomic structure file

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--- 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)

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--- 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

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--- 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

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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.

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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 !
      
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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 !


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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)

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 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

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 Notices:
 Copyright 2020 United States Government as represented by the 
 Administrator of the National Aeronautics and Space Administration. 
 All Rights Reserved.
 
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