1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
|
==================================================================================
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
|
