Updated mdanalaysis script

Author: Shashikant Kumar

ChangeLog

@@ -3,6 +3,15 @@
 -Name
 -changes
 
+--------------
+Oct 15, 2024
+Name: Shashikant Kumar
+Changes: (utils/mdanalysis)
+1. Resolved bugs in SACF calculation
+2. Inter-diffusion routine faster
+3. Added a new example file
+4. Updated the documentation
+
 --------------
 Oct 09, 2024
 Name: Xin Jing

utils/mdanalysis/README.md

@@ -26,7 +26,7 @@ To use the `mdanalysis.py` one needs an input file `carbon.mdanalysis.inpt` whic
  * `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
+ * `BLOCK_LENGTH_SELF_DIFFUSION:` - Block lengths for self diffuison calculation (provide a block length for each elemental specie in the system)
  * `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

utils/mdanalysis/examples/H2O/D_t_0.png

@@ -0,0 +1,11 @@
+t[fs]    D_t
+0.0000E+00 2.3726E-04
+1.0000E-01 4.7454E-04
+2.0000E-01 7.1167E-04
+3.0000E-01 9.4846E-04
+4.0000E-01 1.1848E-03
+5.0000E-01 1.4204E-03
+6.0000E-01 1.6552E-03
+7.0000E-01 1.8890E-03
+8.0000E-01 2.1216E-03
+9.0000E-01 2.3531E-03

utils/mdanalysis/examples/H2O/D_t_0.txt

@@ -0,0 +1,16 @@
+t[fs]    D_t
+0.0000E+00 1.7325E-05
+1.0000E-01 3.4613E-05
+2.0000E-01 5.1860E-05
+3.0000E-01 6.9057E-05
+4.0000E-01 8.6199E-05
+5.0000E-01 1.0328E-04
+6.0000E-01 1.2029E-04
+7.0000E-01 1.3724E-04
+8.0000E-01 1.5410E-04
+9.0000E-01 1.7089E-04
+1.0000E+00 1.8760E-04
+1.1000E+00 2.0423E-04
+1.2000E+00 2.2077E-04
+1.3000E+00 2.3722E-04
+1.4000E+00 2.5359E-04

utils/mdanalysis/examples/H2O/D_t_1.png

@@ -0,0 +1,57 @@
+*************************************************************************** 
+*                   MD analysis (Version 05 Sept 2024)                    *
+*                      Date:  10/15/2024, 09:02:24                        * 
+*************************************************************************** 
+Inputs:
+
+SYSTEM_NAME: H2O	# 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: 0 			# 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: 10 15 	# Block length 
+
+
+INTER_DIFFUSION_FLAG: 1 		# Flag to do inter-diffusion coefficient calculation using integration of VACF
+BLOCK_LENGTH_INTER_DIFFUSION: 20	# Block length
+
+VISCOSITY_FLAG: 1 			# Flag to do shear viscosity calculation using integration of VACF
+BLOCK_LENGTH_VISCOSITY: 20 		# 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]: -2.447001459E+01
+Error bar of internal energy [ha/atom]: 1.487E-03
+*************************************************************************** 
+Pressure (PRES + PRESIG):
+Mean of pressure [GPa]: 4.846579972E+02
+Error bar of pressure [GPa]: 3.127E+00
+*************************************************************************** 
+Self diffusion coefficient:
+Self diffusion coefficients [cm^2/s]: 
+2.3531E-03, 2.5359E-04, 
+Self diffusion coefficients error bar[cm^2/s]: 
+3.5450E-05, 1.3529E-05, 
+*************************************************************************** 
+Inter diffusion coefficient:
+Inter diffusion coefficients [cm^2/s]: 
+9.7906E-03, 
+Inter diffusion coefficients error bar[cm^2/s]: 
+1.8895E-03, 
+*************************************************************************** 
+Shear viscosity:
+Viscosity [Pa-s]: 
+5.4306E-04, 
+Viscosity error bar[Pa-s]: 
+6.4636E-05,