LAMMPS Examples for Hydrocarbons

From EVOCD
(Difference between revisions)
Jump to: navigation, search
 
(4 intermediate revisions by one user not shown)
Line 1: Line 1:
'''Energy minimization of the isobutane (C4H10) molecule:'''
+
== Example 1 ==
  
The initial coordinates of the isobutane (C4H10) molecule are given below. You can copy and paste the information in a file named ''isobutane.dat''.
+
'''Energy minimization of the isobutane (C<sub>4</sub>H<sub>10</sub>) molecule:'''
 +
 
 +
The initial coordinates of the isobutane molecule are given below. You can copy and paste the information in a file named ''isobutane.dat''.
  
 
{|border  ="0"
 
{|border  ="0"
Line 7: Line 9:
  
 
# Sample LAMMPS data file for isobutane (methylpropane) (C4H10)
 
# Sample LAMMPS data file for isobutane (methylpropane) (C4H10)
# This file is used with the LAMMPS input file Isobutane.in
+
# This file is used with the LAMMPS input file isobutane.in
 
# Reference: Physical Chemistry Chemical Physics, 16(13) (2014):6233-6249.
 
# Reference: Physical Chemistry Chemical Physics, 16(13) (2014):6233-6249.
 
# Will reproduce the uncorrected MEAM value for Isobutane in Table 3, Column 4 of the paper.
 
# Will reproduce the uncorrected MEAM value for Isobutane in Table 3, Column 4 of the paper.
Line 50: Line 52:
  
 
# Sample LAMMPS input script for the energy minimization of isobutane (methylpropane) (C4H10)
 
# Sample LAMMPS input script for the energy minimization of isobutane (methylpropane) (C4H10)
# This file is used with the Isobutane.dat file and the MEAM parameter files.
+
# This file is used with the isobutane.dat file and the MEAM parameter files.
 
# Reference: Physical Chemistry Chemical Physics, 16(13) (2014):6233-6249.
 
# Reference: Physical Chemistry Chemical Physics, 16(13) (2014):6233-6249.
 
# Will reproduce the uncorrected MEAM value for Isobutane in Table 3, Column 4 of the paper.  
 
# Will reproduce the uncorrected MEAM value for Isobutane in Table 3, Column 4 of the paper.  
Line 73: Line 75:
 
</pre>
 
</pre>
 
|}
 
|}
 +
 +
 +
[[Category: LAMMPS]]
 +
[[Category: Script]]

Latest revision as of 16:58, 16 April 2015

[edit] Example 1

Energy minimization of the isobutane (C4H10) molecule:

The initial coordinates of the isobutane molecule are given below. You can copy and paste the information in a file named isobutane.dat.


# Sample LAMMPS data file for isobutane (methylpropane) (C4H10)
# This file is used with the LAMMPS input file isobutane.in
# Reference: Physical Chemistry Chemical Physics, 16(13) (2014):6233-6249.
# Will reproduce the uncorrected MEAM value for Isobutane in Table 3, Column 4 of the paper.

14 atoms

-1000.000000 1000.000000 xlo xhi
-1000.000000 1000.000000 ylo yhi
-1000.000000 1000.000000 zlo zhi

2 atom types

Masses

1 12.0111
2 1.0079

Atoms

    1    1    -3.562470    -0.260470    -0.116530
    2    1    -2.438430     0.633300     0.403110
    3    1    -1.077080     0.080400    -0.013190
    4    1    -2.613790     2.064060    -0.101360
    5    2    -4.540900     0.132060     0.180090
    6    2    -3.471380    -1.273370     0.290050
    7    2    -3.542640    -0.331510    -1.209220
    8    2    -2.485530     0.645380     1.498590
    9    2    -0.947440    -0.946270     0.345340
   10    2    -0.267740     0.686240     0.408140
   11    2    -0.964560     0.076010    -1.102550
   12    2    -1.807410     2.708080     0.265230
   13    2    -3.562660     2.484470     0.248610
   14    2    -2.609090     2.104430    -1.195780

The following script performs energy minimization of the isobutane structure. You can save the information in an input file named isobutane.in.


# Sample LAMMPS input script for the energy minimization of isobutane (methylpropane) (C4H10)
# This file is used with the isobutane.dat file and the MEAM parameter files.
# Reference: Physical Chemistry Chemical Physics, 16(13) (2014):6233-6249.
# Will reproduce the uncorrected MEAM value for Isobutane in Table 3, Column 4 of the paper. 

# ------------------ Initialize Simulation -----------------------
clear
units metal
boundary p p p
atom_style atomic
read_data Isobutane.dat

# --------------- Define Interatomic Potential -------------------
pair_style meam
pair_coeff * * CH_library.meam C H CH.meam C H

# -------------------- Define Output -----------------------------
dump coord all custom 1 Isobutane.dump id type x y z

# ------------------- Run Minimization ---------------------------
minimize 1e-25 1e-25 10000 10000

Personal tools
Namespaces

Variants
Actions
home
Materials
Material Models
Design
Resources
Projects
Education
Toolbox