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--- building_a_hydrate_lattice [2018/05/08 11:37] – edit
+++ building_a_hydrate_lattice [2018/05/08 11:48] (current) – edit
@@ Line 39: / Line 39: @@
 **__Using Avicci__**
-You will need to have Java installed to use this program.
+You will need to have Java installed to use this program.  \\
-Click on Avicci.jar to launch the program
+Click on Avicci.jar to launch the program \\
-Specify the inputs:
-- Input path: Enter the absolute path for the .pdb file that contains the coordinates of the oxygen atoms
-- Output path: Enter the absolute path for the .pdb file that will contain the final slab (include the name of the output file in the path)
-- Structure: Enter 1 for structure I or 2 for structure II
-- Fraction Methane in Small Cages: Enter a value between 0 and 1 inclusive (All cages in structure I are considered small cages)
-- Fraction Methane in Large Cages: Enter a value between 0 and 1 inclusive (input ignored for structure I)
-- Fraction Cyclohexane in Large Cages: Enter a value between 0 and 1 inclusive (input ignored for structure I)
-- Fraction Benzene in Large Cages: Enter a value between 0 and 1 inclusive (input ignored for structure I)
-- Water Model ( 1 for TIP4P-EW , 2 for TIP4P-2005 ): Enter 1 or 2
-- Slab Size A: Size of final slab in the X direction as a multiple of the unit cell size, Enter a value greater than zero
-- Slab Size B: Size of final slab in the Y direction as a multiple of the unit cell size, Enter a value greater than zero
-- Slab Size C: Size of final slab in the Z direction as a multiple of the unit cell size, Enter a value greater than zero
-Example: A = 2 , B = 2 , C = 1 creates a 2 X 2 X 1 slab of the unit cell in the input file
-- Number of spaces to 1st coordinate: Number of words/spaces before the x-coordinate in the input .pdb file, used for parsing the coordinates (Enter 5 as the default value)
-Click "Generate Hydrate" to execute the program and close the program. Check the ouptput path for the results of the program.
+__Specify the inputs:__ \\
+- __Input path:__ Enter the absolute path for the .pdb file that contains the coordinates of the oxygen atoms  \\
-(see 4112809_justOxygen_output.cif and 4112807_justOxygen_output.cif)
+- __Output path:__ Enter the absolute path for the .pdb file that will contain the final slab (include the name of the output file in the path)  \\
+- __Structure:__ Enter 1 for structure I or 2 for structure II  \\
+- __Fraction Methane in Small Cages:__ Enter a value between 0 and 1 inclusive (All cages in structure I are considered small cages)  \\
+- __Fraction Methane in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored for structure I)  \\
+- __Fraction Cyclohexane in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored for structure I)  \\
+- __Fraction Benzene in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored for structure I)  \\
+- __Water Model ( 1 for TIP4P-EW , 2 for TIP4P-2005 ):__ Enter 1 or 2  \\
+- __Slab Size A:__ Size of final slab in the X direction as a multiple of the unit cell size, Enter a value greater than zero  \\
+- __Slab Size B:__ Size of final slab in the Y direction as a multiple of the unit cell size, Enter a value greater than zero  \\
+- __Slab Size C:__ Size of final slab in the Z direction as a multiple of the unit cell size, Enter a value greater than zero  \\
+Example: A = 2 , B = 2 , C = 1 creates a 2x2x1 slab of the unit cell in the input file \\
+- __Number of spaces to 1st coordinate:__ Number of words/spaces before the x-coordinate in the input .pdb file, used for parsing the coordinates (Enter 5 as the default value)   \\
+Click "Generate Hydrate" to execute the program and close the program. Check the ouptput path for the results of the program.  \\
+\\
+\\
+If you have any question, feel free to email me at kmanayer(at)yahoo(dot)com  \\