Release Notes

MOMAP 2022B

December 5, 2022

Improvements and new features

  • Add BDF support with MOMAP evc module.
  • Add BDF support with MOMAP transport module.
  • Add bondparam (default to 1.1) for evc, thus bond judgement can be tuned by user.

Bug fixes

  • Fix build-in Dalton mpi parallel running issue.
  • Fix NWChem output handling with ‘Output coordinates in a.u.’.

MOMAP 2022A

April 27, 2022

Improvements and new features

  • Add reorganization energy calculation options by using the four-point method:
    momap_geninp.exe -reorg4p
    Modify momap.inp and then run:
    momap_prep_reorg4p.exe -input mol.com
    Finally, run the job script run.sh to get the reorganization energies.
  • Add parameter module_momap
  • Add walltime_hour for job queue time control
  • Add same_hessian parameter with values 0, 1, and 2, defaut to 0.
    For example, if set to 1, then read hessian only from ffreq(1) in momap.inp, similarly, if set to 2, then read hessian only from ffreq(2) in momap.inp.

Bug fixes

  • fix Turbomole 7.5 output parsing issue.
  • fix PySOC basis set parsing issue.
  • fix ORCA 5 NACME parsing issue.
  • fix transport calculation with Msys2.

MOMAP 2021A

March 31, 2021

New features

  • Add band-like mobility calculation for transport module (in devel stage).

Improvements

  • Increase evc.cart.dat lam output width, thus avoid progrom failure  due to too large lam values.
  • Add some new control parameters, e.g., output_level etc.
  • Re-arrange output files in data directory for transport calculation.

Bug fixes

  • Fix cif file handling issue
  • Fix issues in pysoc calculation
  • Fix oniom file input and output issue
  • Fix Q-Chem NACME unit issue
  • Fix ORCA output parsing issue

MOMAP  Version 2020B

October 16, 2020

New features

  • Reorganization automatic classification and display.
  • INDO support for rapid calculations of large systems.
  • Numerical calculation of transition dipole moments for single molecular/PCM model.
  • Numerical calculation of transition dipole moments for QM/MM model.
  • Automatic calculation of reorganization from quantum chemistry calculation results.
  • Support for ORCA QC package.
  • Support for TeraChem (partially finished). To do: TeraChem lacks NACV or NACME output (expected future version feature of TeraChem)
  • Add V_dynamic_disorder to handle transferintegral disorder, VH*-dyn.dat and/or
    VL*-dyn.dat should be added in data directory.
  • Add HOMO/LUMO dynamic disorder, HOMOLUMO*-dyn.dat should be added in data directory.

Improvements

  • Output oniom input files by setting the 4th bit up (0x08) with parameter data_mol_output_level.
  • Solve the time-consuming problem of reading log file with QM/MM calculation.
  • Add parameter data_mol_output_level to control output of molecular files, default to 0, output files for only one molecule. Setting to a value larger then 0 will output files for all molecules.
  • Reorganize the output data structure, esp., under data directory.

Bug fixes

  • Fix Nonadiabatic couping with empty Electric Field, if the Electric Field is empty, then use ‘Center Atomic Nonadiabatic Coup’ as search string.

MOMAP Version 2020A

March 31, 2020

New features

  • Integration of pysoc to momap.inp, e.g., do_pysoc = 1; &pysoc … /,  put needed outputs to file pysoc_out.dat, other files are moved to data directory.
  • Add job_slot_limit parameter for job control in HPC environment, e.g.,  if set to 4, means we can run a maximum of 4 jobs at most.
  • Add RE_use_neutral_chk parameter in transport calculation, to optimize anion and cation state geometry from chk output of neutral state geometry if set to 1.
  • Add RE_calc_lambda_4P parameter, to do four point reorganization energy calculations if set.
  • Integration of PySOC package.
  • Integration of Dalton 2018.0 package.
  • Add use_evc_dint = 1 to use evc.dint.dat for NM calculation if the calculated reorganization energy is found too large.
  • Add use_moo flag to control if Zindos uses moo_overlap.exe to do quick calculations. If use_moo is not set (default to 0), then Zindos is done with normal HL calculations.

Improvements

  • Add thinfilm transport calculation support.
  • Add ZINDO support for rapid calculations of large systems.
  • Extend output of transport_gatherdata.exe.
  • Support for multiple QM/MM input formats, can be empty space delimited, or comma delimited (e.g., when geom=check is used in Gaussian input file).
  • Output mol*_neighbors_mid.cif for molecular identification, a virtual atom  (mol_id) is added at the Center Of Mass (COM).
  • Add plot_transint_V.py to plot neighbor’s mols with transfer integral values.
  • Add utilities transport_cif2mol.exe, transport_cif2gjf.exe and transport_cif2xyz.exe etc.
  • Add ratetype and evc_type option check, thus avoid input typo error.
  • Add Output hoprates.dat in MC run directories.
  • Add gnuplot scripts to directly generate png files (pngcairo terminal).
  • Add applied electric field support in hoprate calculation.

Bug fixes

  • Fix python 3 compatibility issue, now MOMAP works with both python 2 and 3.
  • Fix manager scripts momap (old style) and momap.py.
  • Fix jobidstr of transport_prepare.exe to dynamic allocation to avoid out of memory bound.
  • Fix chargetype input option, now ‘a’, ‘e’ or ‘h’ option works correctly.
  • Fix IEEE_OVERFLOW_FLAG IEEE_DENORMAL issue, delete unused InvZ which results in too large a value that a double can hold.

MOMAP Version 2019B

October 9, 2019

New features

  • Support enlarged unitcell system, preparing for amorphous system.
  • Add parameter nodelist for scheduling systems.
  • Add various handy scripts in scripts directory.
  • Add normal termination check from QC calculations.
  • Imaginary frequency check from QC calculations.
  • Add transport_cif_split.exe, transport_cif_expand.exe etc. for input crystal file manipulation.
  • Add env.sh and env.csh for running environment settings, user can use the environment setting in, for example, ~/.bashrc.
  • Improve installation with user input for installation path, thus MOMAP  package can be installed to any location.

MOMAP Version 2019A

May 8, 2019

New features

  • New python version job manager momap.py.
  • Reasonableness check to reorganization calcuation.
  • Add interface to Q-Chem package.
  • Support of QM/MM calculations, e.g., the Gaussian oniom model.
  • Transport mobility calculation with multi-component system.
  • Transport module rewritten in C/C++ and python.
  • Transport module supports cif with all space groups.
  • Transport module supports commonly used scheduling systems, e.g.,  LSF, PBS, SLURM and LOCAL.
  • Significant performance improvement to transport module, now a normal tranport run can be finished in less than 10 minutes depending on the computing power.

MOMAP Version 1.0.0

April 14, 2017

New features

  • Add the transport module

MOMAP Version 0.2.005

November 29, 2014

New features

  • Add the dimer spectra and rate codes which based on Correlation functions and Fourier transform
  • Add the dimer spectra0 code which based on the  sum of states

MOMAP Version 0.2.004

November 23, 2014

New features

  • Debug for Dushinsky Calculate

MOMAP Version 0.2.003

June 17, 2014

New features

  • Add the support for quadruple precision algorithm in the codes of ic and spectra.
  • Add spectra0 code which can calculate zero temperature absorption and fluorescence spectra in displaced-distorted Harmonic oscillator approximation
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