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It is redesign last version of Appa (Martin Alexandre)
================================================================================== WHAT IS ABINT POST-PROCESS APPLICATION (APPA) ? APPA is a graphical (or text) post-processor for ABINIT dedicated to the analysis of Molecular Dynamics output files (trajectories). Output files from large scale molecular dynamics simulations are not easy to manage. All the data can be extracted from output files in NetCDF or ACSCII(text) formats. APPA is a graphical tool written in python (PyQt4 library) able to read ABINIT output, easy to use in order to follow a trajectory from molecular dynamics simulation (total energy, pressure...). It is also possible to calculate velocity autocorrelation function from the simulation, radial pair distribution, vibrational density of states, etc.... If Python is able to handle efficiently these kinds of output files, this one is not suited to compute some quantities coming from large-scale MD simulation. That?s why APPA also uses Fortran, and thanks to the F2PY library, the connection between these both languages is possible. ================================================================================== INSTALLATION Requirements: python version >= 2.7 PyQT4 Numpy To take benefit from optimized computational routines written in Fortran: cd fortran f2py -c math.f90 --fcompiler='gfortran' -m math f2py -c topology.f90 --fcompiler='gfortran' -m topology f2py -c positions.f90 --fcompiler='gfortran' -m positions ================================================================================== RUNNING APPA With a Graphical User Interface: appa.py Text version: appa_nw.py ================================================================================== COMMAND LINE INTERFACE #The "text" version can be used via an input file. #This input file must have extension ".APPA". #Launch it by: appa_nw.py input.APPA #List of Input Keywords: # file #Give the path of your output file # stepmin #Give the initial step of your simulation (-1 for minimum step) # stepmax #Give the final step of your simulation (-1 for maximum step) # potential_energy #Print the potential energy # total_energy #Print the total energy # kinetic_energy #Print the kinetic_energy # temperature #Print the temperature # pressure #Print the pressure # stress #Print the stress # vacf #Compute velocity autoceraltion function # vdos #Compute vibrational density of state # vdosres #Give the resolution for the gaussian (between 1 and 100) #You can select the output file format by appending 1,2 or 3 after the keyword: # stress 1 # PDF format # stress 2 # ASCII format # stress 3 # PDF + ASCII # stress # PDF + ASCII #EXEMPLE: #output 1 file Al.out stepmin 1 stepmax 1000 potential_energy 2 total_energy 2 kinetic_energy temperature 1 pressure stress 3 vacf 2 vdos 2 rdf 2 vdosres 8 #output 2 file Al_1o_HIST stepmin -599 stepmax 95959000 total_energy 2 temperature stress 3 vdosres 1
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