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04-26-2019

ALADYN mini-app is a simple molecular dynamics (MD) code for performing 
constant energy atomistic simulations using artificial neural networks 
(ANN) interatomic potential trained for Al crystal structure.
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.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.test

Running a tets case:
> aladyn              ! executes 10 MD steps reporting at each step
> aladyn -n 100 -m 10 ! executes 100 MD steps, reporting every 10-th step

Available PBS scripts used for NASA/LaRC K3 cluster:
ALADYN_intel.job      - run the intel version
ALADYN_pgi_V100.job   - run the pgi version with OpneACC for V100 gpu.

Screen output is riderected to aladyn.out

Example outputs are saved in: aladyn_intel.out and aladyn_pgi.out
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INPUT FILES:

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

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--- Available test structures in directory STR:

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:

   aladyn.f       - Main program
   aladyn_sys.f, aladyn_sys_OMP.f, aladyn_sys_NO_OMP.f - system modules
   aladyn_mods.f  - general purpose modules
   aladyn_IO.f    - I/O operations module

   aladyn_ANN.f   - ANN potential energy and force calculation module
    contains:
     subroutine Frc_ANN_OMP  ! force & energy calculation (OpenMP version)
     subroutine Frc_ANN_ACC  ! force & energy calculation (OpenACC version)

   aladyn_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


 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: [email protected]



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 Notices:
 Copyright 2018 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 
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 INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE ERROR 
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 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. 
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 AND DISTRIBUTES IT "AS IS."

 
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 RECIPIENT.  IF RECIPIENT'S USE OF THE SUBJECT SOFTWARE RESULTS IN ANY 
 LIABILITIES, DEMANDS, DAMAGES, EXPENSES OR LOSSES ARISING FROM SUCH
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 RECIPIENT'S USE OF THE SUBJECT SOFTWARE, RECIPIENT SHALL INDEMNIFY AND
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