Added mdanalysis postprocessing code

ChangeLog

@@ -3,6 +3,15 @@
 -Name
 -changes
 
+--------------
+September 09, 2024
+Name: Shashikant Kumar
+Changes: (utils/mdanalysis)
+1. Python post processing for MD analysis
+1. Included plotting 
+2. Simplified the inter-diffusion 
+
+
 --------------
 September 05, 2024
 Name: Shashikant Kumar

utils/mdanalysis/README.md

@@ -0,0 +1,49 @@
+# `mdanalysis` – Post processing of MD 
+
+## Overview
+
+`mdanalysis.py` is a Python script that provides a set of tools for processing MD trajectory files generated by [**SPARC**](https://github.com/SPARC-X/SPARC/) and calculating various quantities such as total internal energy, total pressure, self-diffusion coefficient, inter-diffusion coefficient, shear viscosity, and pair-correlation funcions.
+
+## Requirements
+
+To use `mdanalysis.py`, you need the following:
+
+- Python 3.6 or later
+- Numpy
+
+
+## Usage
+```shell
+$ python mdanalysis.py carbon.mdanalysis.inpt
+```
+To use the `mdanalysis.py` one needs an input file `carbon.mdanalysis.inpt` which contains the following variables. 
+ * `SYSTEM_NAME:` - Name of the system. This will determine the names of the file (e.g. C2.out, C2.aimd, C2.out_01 etc)
+ * `N_FOLDERS:` - Number of folders used to run the simulation (Each folder will be considered a MD trajectory with an indepedent starting point)
+ * `FOLDER_PATH_SIMULATIONS:` - Location of the folders
+ * `N_SIMULATIONS_FOLDER:` -Number of simulation run within each folder (If it has 3 simulations, C2.out, C2.out_01, C2.out_02 files are expected.)
+ * `N_EQUIL:` - Number of MD steps for equilibriation
+ * `PCF_FLAG:` - Flag to do a pair correlation function calculation
+ * `RANGE_PCF:` - Maximum radial distance to be  considered 
+ * `SIZE_HIST_PCF:` - Total number of spherical shells to be considered
+ * `SELF_DIFFUSION_FLAG:` - Flag to do self-diffusion coefficient calculation using integration of VACF
+ * `BLOCK_LENGTH_SELF_DIFFUSION:` - Block length for self diffuison calculation
+ * `INTER_DIFFUSION_FLAG:` - Flag to do inter-diffusion coefficient calculation using integration of VACF
+ * `BLOCK_LENGTH_INTER_DIFFUSION:` - Block length for inter diffuison calculation
+ * `VISCOSITY_FLAG:` - Flag to do shear viscosity calculation using integration of VACF
+ * `BLOCK_LENGTH_VISCOSITY:` - Block length for viscosity calculation
+ * `INTERNAL_ENERGY_FLAG:` - Flag to get the mean and error bar of total internal energy (ha/atom)
+ * `PRESSURE_FLAG:` - Flag to get the mean and error bar of total pressure (GPa)
+
+An output file named `carbon.mdanalysis.out` will be written with all the values.
+## Usage
+ * The inter-diffusion coefficient has only been implemented for binary systems. 
+ * The error bar has been calculated using the re-blocking method (https://web.ornl.gov/~kentpr/thesis/pkthnode31.html). The data for the standard deviation, block-size is also written in a text file. Please check these files to ensure that the standard deviations have reached close to limiting values
+ * For diffusion coefficients and viscosity, velocity autocorrelation function (VACF) and stress autocorrelation function (SACF) has also been written in files `vacf.txt` and `sacf.txt`. Check these files to make sure that they have decayes to zero for the specified block length. 
+ * The block length for diffusion coefficients and viscosity calculation needs to be tuned by the user such that the corresponding auto-correlation functions have decayed to zero.
+
+## Example
+
+Explore an example of how to use `mdanalysis` to calculate for a dummy carbon system in the `example/` directory.
+
+
+

utils/mdanalysis/example/D_t_0.txt

@@ -0,0 +1,101 @@
+t[fs]    D_t
+0.0000E+00 2.7258E-04
+4.0000E-02 5.4509E-04
+8.0000E-02 8.1743E-04
+1.2000E-01 1.0895E-03
+1.6000E-01 1.3611E-03
+2.0000E-01 1.6321E-03
+2.4000E-01 1.9025E-03
+2.8000E-01 2.1721E-03
+3.2000E-01 2.4408E-03
+3.6000E-01 2.7085E-03
+4.0000E-01 2.9752E-03
+4.4000E-01 3.2406E-03
+4.8000E-01 3.5048E-03
+5.2000E-01 3.7676E-03
+5.6000E-01 4.0290E-03
+6.0000E-01 4.2888E-03
+6.4000E-01 4.5470E-03
+6.8000E-01 4.8035E-03
+7.2000E-01 5.0583E-03
+7.6000E-01 5.3113E-03
+8.0000E-01 5.5625E-03
+8.4000E-01 5.8117E-03
+8.8000E-01 6.0590E-03
+9.2000E-01 6.3044E-03
+9.6000E-01 6.5477E-03
+1.0000E+00 6.7889E-03
+1.0400E+00 7.0281E-03
+1.0800E+00 7.2651E-03
+1.1200E+00 7.5000E-03
+1.1600E+00 7.7328E-03
+1.2000E+00 7.9633E-03
+1.2400E+00 8.1917E-03
+1.2800E+00 8.4180E-03
+1.3200E+00 8.6420E-03
+1.3600E+00 8.8638E-03
+1.4000E+00 9.0834E-03
+1.4400E+00 9.3007E-03
+1.4800E+00 9.5159E-03
+1.5200E+00 9.7288E-03
+1.5600E+00 9.9395E-03
+1.6000E+00 1.0148E-02
+1.6400E+00 1.0354E-02
+1.6800E+00 1.0558E-02
+1.7200E+00 1.0760E-02
+1.7600E+00 1.0960E-02
+1.8000E+00 1.1158E-02
+1.8400E+00 1.1353E-02
+1.8800E+00 1.1547E-02
+1.9200E+00 1.1738E-02
+1.9600E+00 1.1927E-02
+2.0000E+00 1.2114E-02
+2.0400E+00 1.2299E-02
+2.0800E+00 1.2481E-02
+2.1200E+00 1.2662E-02
+2.1600E+00 1.2841E-02
+2.2000E+00 1.3018E-02
+2.2400E+00 1.3193E-02
+2.2800E+00 1.3366E-02
+2.3200E+00 1.3536E-02
+2.3600E+00 1.3705E-02
+2.4000E+00 1.3872E-02
+2.4400E+00 1.4038E-02
+2.4800E+00 1.4201E-02
+2.5200E+00 1.4363E-02
+2.5600E+00 1.4522E-02
+2.6000E+00 1.4680E-02
+2.6400E+00 1.4836E-02
+2.6800E+00 1.4991E-02
+2.7200E+00 1.5143E-02
+2.7600E+00 1.5294E-02
+2.8000E+00 1.5444E-02
+2.8400E+00 1.5591E-02
+2.8800E+00 1.5737E-02
+2.9200E+00 1.5882E-02
+2.9600E+00 1.6024E-02
+3.0000E+00 1.6166E-02
+3.0400E+00 1.6305E-02
+3.0800E+00 1.6443E-02
+3.1200E+00 1.6580E-02
+3.1600E+00 1.6715E-02
+3.2000E+00 1.6849E-02
+3.2400E+00 1.6981E-02
+3.2800E+00 1.7112E-02
+3.3200E+00 1.7241E-02
+3.3600E+00 1.7369E-02
+3.4000E+00 1.7495E-02
+3.4400E+00 1.7621E-02
+3.4800E+00 1.7744E-02
+3.5200E+00 1.7867E-02
+3.5600E+00 1.7988E-02
+3.6000E+00 1.8108E-02
+3.6400E+00 1.8227E-02
+3.6800E+00 1.8344E-02
+3.7200E+00 1.8460E-02
+3.7600E+00 1.8575E-02
+3.8000E+00 1.8689E-02
+3.8400E+00 1.8802E-02
+3.8800E+00 1.8913E-02
+3.9200E+00 1.9023E-02
+3.9600E+00 1.9132E-02

utils/mdanalysis/example/block_error_D.txt

@@ -0,0 +1,5 @@
+1.000000E+00   1.868896E-02   9.844698E-05
+2.000000E+00   1.868896E-02   1.375621E-04
+4.000000E+00   1.868856E-02   1.910072E-04
+8.000000E+00   1.868856E-02   2.291131E-04
+1.600000E+01   1.866421E-02   2.360276E-04

utils/mdanalysis/example/block_error_IEN.txt

@@ -0,0 +1,9 @@
+block-length    mean    std-dev
+1.000E+00 -5.879E+01 2.572E-01
+2.000E+00 -5.879E+01 2.536E-01
+4.000E+00 -5.879E+01 2.730E-01
+8.000E+00 -5.878E+01 3.229E-01
+1.600E+01 -5.877E+01 3.948E-01
+3.200E+01 -5.874E+01 4.953E-01
+6.400E+01 -5.874E+01 6.371E-01
+1.280E+02 -5.863E+01 6.983E-01

utils/mdanalysis/example/block_error_pressure.txt

@@ -0,0 +1,9 @@
+block-length    mean    std-dev
+1.000E+00 3.293282E+04 1.714E+01
+2.000E+00 3.293282E+04 2.413E+01
+4.000E+00 3.293075E+04 3.382E+01
+8.000E+00 3.292659E+04 4.689E+01
+1.600E+01 3.291819E+04 6.301E+01
+3.200E+01 3.290485E+04 7.374E+01
+6.400E+01 3.290485E+04 8.589E+01
+1.280E+02 3.293060E+04 1.058E+02

utils/mdanalysis/example/block_error_viscosity.txt

@@ -0,0 +1,3 @@
+1.000000E+00   1.383397E-02   2.736892E-03
+2.000000E+00   1.383397E-02   3.620604E-03
+4.000000E+00   1.274491E-02   3.574479E-03

utils/mdanalysis/example/carbon.MDanalysis.out

@@ -0,0 +1,56 @@
+*************************************************************************** 
+*                   MD analysis (Version 05 Sept 2024)                    *
+*                      Date:  09/09/2024, 07:07:25                        * 
+*************************************************************************** 
+Inputs:
+
+SYSTEM_NAME: carbon						# Name of the system. This will determine the names of the file (e.g. C2.out, C2.aimd, C2.out_01 etc)
+N_FOLDERS: 1 						# Number of folders used to run the simulation (Each folder will be considered a MD trajectory with an indepedent starting point)
+FOLDER_PATH_SIMULATIONS: ./				# Location of the folders
+N_SIMULATIONS_FOLDER: 1 					# Number of simulation run within each folder (If it has 3 simulations, C2.out, C2.out_01, C2.out_02 files are expected.)
+
+
+N_EQUIL: 10				# Number of MD steps for equilibriation
+
+
+PCF_FLAG: 1 						# Flag to do a pair correlation function calculation
+RANGE_PCF: 10 						# Maximum radial distance to be  considered 
+SIZE_HIST_PCF: 100 				# Total number of spherical shells to be considered
+
+SELF_DIFFUSION_FLAG: 1 				# Flag to do self-diffusion coefficient calculation using integration of VACF
+BLOCK_LENGTH_SELF_DIFFUSION: 100 	# Block length 
+
+
+INTER_DIFFUSION_FLAG: 0 			# Flag to do inter-diffusion coefficient calculation using integration of VACF
+BLOCK_LENGTH_INTER_DIFFUSION: 100	# Block length
+
+VISCOSITY_FLAG: 1 					# Flag to do shear viscosity calculation using integration of VACF
+BLOCK_LENGTH_VISCOSITY: 100 		# Block length
+
+INTERNAL_ENERGY_FLAG: 1 			# Flag to get the mean and error bar of total internal energy (ha/atom)
+PRESSURE_FLAG: 1 					# Flag to get the mean and error bar of total pressure (GPa)
+
+
+*************************************************************************** 
+Internal energy (UEN + KENIG):
+Mean of internal energy [ha/atom]: -5.879440854E+01
+Error bar of internal energy [ha/atom]: 2.536E-01
+*************************************************************************** 
+Pressure (PRES + PRESIG):
+Mean of pressure [GPa]: 3.293282311E+04
+Error bar of pressure [GPa]: 4.689E+01
+*************************************************************************** 
+Self diffusion coefficient:
+Self diffusion coefficients [cm^2/s]: 
+1.8689E-02, 
+Self diffusion coefficients error bar[cm^2/s]: 
+1.3756E-04, 
+*************************************************************************** 
+Shear viscosity:
+Viscosity [Pa-s]: 
+1.3834E-02, 
+Viscosity error bar[Pa-s]: 
+3.6206E-03, 
+*************************************************************************** 
+Pair correlation function:
+Pair correlation function written!!