nap - v250814

• fix some nappy scripts to match the new output format in pmd.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys 7 months ago

nap - v250715

• implement prior-knowledge-incorporated uf3l.
• set version number same as the revision tag.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys 8 months ago

nap - v0.13.3

• fix pyproject.toml for installing napsys command

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys 9 months ago

nap - v0.13.2

• fix bugs in example/fitpotDNNSiO
• fix bugs that appear with intel compilers
• change nappy installation from setup.py to pyproject.toml

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys 9 months ago

nap - v0.13.1

• fix a bug in UF3L potential (parallel implementation)
• modify MSD related nappy scripts to be compatible to combined trajectory file

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys 10 months ago

nap - v0.13.0

• change default output format for trajectory as one extxyz-format file.
• implement UF3L potential
• some minor changes and bug fixes

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys 10 months ago

nap - v0.12.2

• Implemented UF3 force field.
• Fix a bug consistency in data type between pandas and numpy.
• Minor bug fixes.

Full Changelog: https://github.com/ryokbys/nap/compare/rev240722...rev241006

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 1 year ago

nap - v0.12.1

• fix a fatal bug of a lost file in the previous version.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 1 year ago

nap - v0.12.0

• change the definition of each digit in the atom tag.
• implement grouping functionality.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 1 year ago

nap - v0.11.2

• modify the name of ASE calculator as PMDASECalculator
• fix a fatal performance issue in PMDASECalculator

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys almost 2 years ago

nap - v0.11.1

• fix: backward compatibility to old-style pmdini file

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys almost 2 years ago

nap - v0.11.0

• change the pmd-format style (particulary h-matrix part)
• implement combined pmd/dump output from pmd

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys almost 2 years ago

nap - v0.10.23

Changes: - vector component constraint - center of mass analysis in msd.py and vacf.py - modify pmd-format to include some system info at header - remove {erg,frc,strs}.pmd from output

Bug fixes: - fix not to read strs.pmd in elasticity.py - fix mklsprsngl which could affect some python programs.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 2 years ago

nap - v0.10.22

• Fixed a bug in mklsprsngl that is called from python scripts. This could affect some important scripts for optimizing force-field parameters such as rdf.py and adf.py. Please be careful when updating to this version.
• Removed output files, erg.pmd, frc.pmd and strs.pmd at the end of pmd run. Instead, those information are stored in pmdfin file.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 2 years ago

nap - v0.10.21

• change: the style of stress_target entry
• implement: read gzipped file in nappy.
• fix: fail in examples/pmd_parallel
• fix: scaled velocity change in repeating the system in nappy
• fix: bug in velocity conversion real <==> scaled
• fix: wrong order of velocity component in dump format output.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys almost 3 years ago

nap - v0.10.20

• fix some bugs
• implement OpenMP in force_Tersoff
• implement OpenACC only in force_LJ

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys almost 3 years ago

nap - v0.10.19

• fix some bugs in rdf.py and adf.py when using with --fortran option.
• remove pmods package from nappy/pmd.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 3 years ago

nap - v0.10.18

• fix bugs in fitpot related to changes made before...

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 3 years ago

nap - v0.10.17

• let pmd automatically change the number of neighbors, number of boundary atoms (and thus the number of atoms) during MD
• store information of the above and write out at the end of MD

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 3 years ago

nap - v0.10.16

• fix a fatal bug in colorcharge NEMD that is introduced since I don't remember...

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 3 years ago

nap - v0.10.15

• add lflux_utils.py for analysing local flux output
• fix bugs in examples/fp_XXX
• fix some bugs

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 3 years ago

nap - v0.10.14

• implemented RFMEAM potential.
• implemented strain control using deform entry.
• fixed some bugs.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys almost 4 years ago

nap - v0.10.13

• Implement TPE and weighted TPE (named WPE) in fp.py.
• Fix minor bugs in fp.py

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 4 years ago

nap - v0.10.12

• Add setup.py for installing nappy.
• Re-implemented SGD in fitpot.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 4 years ago

nap - v0.10.11

• fixed a minor bug in cs.py that could occur after many generations.
• fixed a bug that could occur when importing nappy without pmd_wrapper compiled.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 4 years ago

nap - v0.10.10

• implemented OpenMP for pairlist and some forces.
• implemented memory module.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 4 years ago

nap - v0.10.9

• added memory module for used memory information in pmd
• improved the efficiency in fp.py by performing random candidates at the same time with updated candidates.
• fixed the timing of removal of translational motion in order to make it work strictly in pmd.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 4 years ago

nap - v0.10.8

• not reallocate namax related arrays in default
• bug fixes about napsys.makepairlist

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys almost 5 years ago

nap - v0.10.7

• Species probability density inside subsystem.
• Fortran MD and pair-list routines are callable from python.
• Species neutron scattering length can be specified in rdf.py.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys almost 5 years ago

nap - v0.10.6

• Fixed some bugs in rdf.py, so one is recommended to use newer than this version when one uses fp.py. But fp.py should work correctly if one uses the same version of rdf.py to make RDFs of both reference system and trial system.
• rdf.py can calculate total g(r) by weighted sum of species-pair g(r)'s which corresponds to experimental S(Q) obtained by neutron scattering.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 5 years ago

nap - v0.10.5

• implemented 1D-TTM as a heat conducting medium attached to 3D TTM-MD.
• introduced print_level
• changed default sorting algorithm for efficiency

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 5 years ago

nap - v0.10.4

• minor changes in JOSS paper.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 5 years ago

nap - v0.10.3

• merged JOSS branch

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 5 years ago

nap - v0.10.2

• added examples/pmd_parallel for testing parallel execution of pmd.
• corrected a bug making pmd and fitpot from the nap root directory.
• replaced mk_lspr.F90 with pairlist module
• added time module

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 5 years ago

nap - v0.10.1

• added test entry in makefile in examples and also in makefiles for nap, pmd, fitpot.
• implemented local flux in pmd.
• implemented probability density of ions during MD.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys about 5 years ago

nap - v0.9.2

• Add READMEs in examples.
• Modify documentation.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 5 years ago

nap - v0.9.1

• Tidied up example files.

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 5 years ago

nap - v0.9.0

Scientific Software - Peer-reviewed - Fortran
Published by ryokbys over 5 years ago