deploy: fa9e5dd

avatars/level3/water-adsorption-in-silica/SiO.1990.vashishta

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+# DATE: 2015-10-14 UNITS: metal CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: P. Vashishta, R. K. Kalia, J. P. Rino, and I. Ebbsjo, Phys. Rev. B 41, 12197 (1990).
+#
+# Vashishta potential file for SiO2, P. Vashishta, R. K. Kalia, J. P. Rino, and I. Ebbsjo,
+# Phys. Rev. B 41, 12197 (1990).
+# 
+# These parameters, some inferred indirectly, give a good
+# match to the energy-volume curve for alpha-quartz in Fig. 2 of the paper.
+#
+# These entries are in LAMMPS "metal" units:
+#   H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge); 
+#   lambda1, lambda4, rc, r0, gamma = Angstroms; 
+#   D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV; 
+#   other quantities are unitless
+#
+# element1  element2  element3
+#           H  eta  Zi  Zj  lambda1  D  lambda4
+#           W  rc  B  gamma  r0  C  cos(theta)
+
+Si  Si  Si  0.82023  11  1.6  1.6  999  0.0  4.43
+            0.0  10.0  0.0  0.0  0.0  0.0  0.0
+
+O   O   O   743.848  7  -0.8 -0.8 999  22.1179  4.43
+            0.0  10.0  0.0  0.0  0.0  0.0  0.0
+
+O   Si  Si  163.859  9  -0.8  1.6  999  44.2357  4.43
+            0.0  10.0  20.146  1.0  2.60  0.0  -0.77714596
+
+Si  O   O   163.859  9  1.6  -0.8  999  44.2357  4.43
+            0.0  10.0  5.0365  1.0  2.60  0.0  -0.333333333333
+
+Si  O   Si  0.0  0.0  0.0  0.0  0.0  0.0  0.0
+            0.0  0.0  0.0  0.0  0.0  0.0  0.0
+
+Si  Si  O   0.0  0.0  0.0  0.0  0.0  0.0  0.0
+            0.0  0.0  0.0  0.0  0.0  0.0  0.0            
+
+O   Si  O   0.0  0.0  0.0  0.0  0.0  0.0  0.0
+            0.0  0.0  0.0  0.0  0.0  0.0  0.0
+
+O   O   Si  0.0  0.0  0.0  0.0  0.0  0.0  0.0
+            0.0  0.0  0.0  0.0  0.0  0.0  0.0

avatars/level3/water-adsorption-in-silica/TIP4P2005.txt

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+# Water molecule.
+
+3 atoms
+2 bonds
+1 angles
+
+Coords
+
+1    0 0 0
+2    0.9584 0 0
+3    -0.23996 0.92787 0
+
+Types
+
+1        3
+2        4
+3        4
+
+Charges
+
+1       -1.1128
+2        0.5564
+3        0.5564
+
+Bonds
+
+1   1      1      2
+2   1      1      3
+
+Angles
+
+1   1      2      1      3
+
+Shake Flags
+
+1 1
+2 1
+3 1
+
+Shake Atoms
+
+1 1 2 3
+2 1 2 3
+3 1 2 3
+
+Shake Bond Types
+
+1 1 1 1
+2 1 1 1
+3 1 1 1
+
+Special Bond Counts
+
+1 2 0 0
+2 1 1 0
+3 1 1 0
+
+Special Bonds
+
+1 2 3
+2 1 3
+3 1 2

avatars/level3/water-adsorption-in-silica/input.lammps

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+# LAMMPS input script
+# author : Simon Gravelle
+# lammpstutorials.github.io
+
+units metal
+boundary p p p
+atom_style full
+neighbor 1.0 bin
+neigh_modify delay 1
+pair_style hybrid/overlay vashishta lj/cut/tip4p/long 3 4 1 1 0.1546 10
+kspace_style pppm/tip4p 1.0e-4
+bond_style harmonic
+angle_style harmonic
+
+read_data SiOwithwater.data
+molecule h2omol TIP4P2005.txt
+lattice sc 3
+create_atoms 0 box mol h2omol 45585
+lattice none 1
+
+group SiO type 1 2
+group H2O type 3 4
+
+pair_coeff * * vashishta SiO.1990.vashishta Si O NULL NULL
+pair_coeff * * lj/cut/tip4p/long 0 0
+pair_coeff 1 3 lj/cut/tip4p/long 0.0057 4.42 # epsilonSi = 0.00403, sigmaSi = 3.69
+pair_coeff 2 3 lj/cut/tip4p/long 0.0043 3.12 # epsilonO = 0.0023, sigmaO = 3.091
+pair_coeff 3 3 lj/cut/tip4p/long 0.008 3.1589
+pair_coeff 4 4 lj/cut/tip4p/long 0.0 0.0
+bond_coeff 1 0 0.9572
+angle_coeff 1 0 104.52
+
+fix shak H2O shake 1.0e-4 200 0 b 1 a 1 mol h2omol
+
+compute_modify thermo_temp dynamic yes
+compute ctH2O H2O temp
+compute_modify ctH2O dynamic yes
+fix mynvt1 H2O nvt temp 300 300 0.1
+fix_modify mynvt1 temp ctH2O
+compute ctSiO SiO temp
+fix mynvt2 SiO nvt temp 300 300 0.1
+fix_modify mynvt2 temp ctSiO
+timestep 0.001
+thermo 1000
+
+region forvideo block -3 23 5 19 5 16
+group in region forvideo
+group water_in intersect H2O in 
+group water_in include molecule
+group SiO_in intersect SiO in
+group forvideo union water_in SiO_in
+
+dump dmp forvideo atom 5 dump.lammpstrj
+
+run 2000

avatars/level3/water-adsorption-in-silica/numbermolecule.dat

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+# Time-averaged data for fix myat1
+# TimeStep v_nO

index.html

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                                 </div>
                             </a>
                         </article>
+                        <!--
+                        <article class="style1">
+                            <span class="image">
+                                <img src="avatars/level3/water-adsorption-in-silica/avatar-GCMC-LAMMPS.png" alt="" />
+                            </span>
+                            <a href="sphinx/build/html/tutorials/level3/water-adsorption-in-silica.html">
+                                <div class="content">
+                                    <p align="left">
+                                        Using <b>GCMC</b> to adsorb water in a nanopore
+                                    </p>
+                                </div>
+                            </a>
+                        </article>
+                        -->
                     </section>
                 </div>
             </div>