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.nb
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.nb
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(************** Content-type: application/mathematica **************
Mathematica-Compatible Notebook
This notebook can be used with any Mathematica-compatible
application, such as Mathematica, MathReader or Publicon. The data
for the notebook starts with the line containing stars above.
To get the notebook into a Mathematica-compatible application, do
one of the following:
* Save the data starting with the line of stars above into a file
with a name ending in .nb, then open the file inside the
application;
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clipboard, then use the Paste menu command inside the application.
Data for notebooks contains only printable 7-bit ASCII and can be
sent directly in email or through ftp in text mode. Newlines can be
CR, LF or CRLF (Unix, Macintosh or MS-DOS style).
NOTE: If you modify the data for this notebook not in a Mathematica-
compatible application, you must delete the line below containing
the word CacheID, otherwise Mathematica-compatible applications may
try to use invalid cache data.
For more information on notebooks and Mathematica-compatible
applications, contact Wolfram Research:
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Wolfram Research.
*******************************************************************)
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\(ElectrostaticVirial[mol1_, atom1_] :=
Module[{fx, fy, fz, i, j, vir},
vir = 0; \[IndentingNewLine]Do[
If[j \[NotEqual]
mol1 || \((IntraMol[j] \[Equal] False && j \[Equal] mol1 &&
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positionatom[mol1, atom1], positionatom[j, i]])\))\)
CoulombForce[q[mol1, atom1], q[j, i],
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positionatom[j,
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positionatom[mol1, atom1], positionatom[j, i]])\))\)
CoulombForce[q[mol1, atom1], q[j, i],
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positionatom[j,
i]]]; \[IndentingNewLine]fz = \((\((positionatom[j,
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positionatom[mol1, atom1], positionatom[j, i]])\))\)
CoulombForce[q[mol1, atom1], q[j, i],
Distance[positionatom[mol1, atom1], positionatom[j, i]]];
vir -= {fx, fy,
fz} . \((positionatom[j, i] -
positionatom[mol1, atom1])\)], {j, 1,
Length[positions]}, {i, 1,
Length[positions[\([j]\)]]}]; {vir}]\), "\[IndentingNewLine]",
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\(ElectrostaticStress[mol1_, atom1_] :=
Module[{fx, fy, fz, i, j, stress},
stress = {{0, 0, 0}, {0, 0, 0}, {0, 0, 0}}; \[IndentingNewLine]Do[
If[j \[NotEqual]
mol1 || \((IntraMol[j] \[Equal] False && j \[Equal] mol1 &&
i \[NotEqual] atom1)\),
fx = \((\((positionatom[j, i] -
positionatom[mol1, atom1])\)[\([1]\)]/\((Distance[
positionatom[mol1, atom1], positionatom[j, i]])\))\)
CoulombForce[q[mol1, atom1], q[j, i],
Distance[positionatom[mol1, atom1],
positionatom[j,
i]]]; \[IndentingNewLine]fy = \((\((positionatom[j,
i] - positionatom[mol1,
atom1])\)[\([2]\)]/\((Distance[
positionatom[mol1, atom1], positionatom[j, i]])\))\)
CoulombForce[q[mol1, atom1], q[j, i],
Distance[positionatom[mol1, atom1],
positionatom[j,
i]]]; \[IndentingNewLine]fz = \((\((positionatom[j,
i] - positionatom[mol1,
atom1])\)[\([3]\)]/\((Distance[
positionatom[mol1, atom1], positionatom[j, i]])\))\)
CoulombForce[q[mol1, atom1], q[j, i],
Distance[positionatom[mol1, atom1],
positionatom[j,
i]]]; \[IndentingNewLine]stress -= {{fx \((positionatom[
j, i] - positionatom[mol1, atom1])\)[\([1]\)],
fy \((positionatom[j, i] -
positionatom[mol1, atom1])\)[\([1]\)],
fz \((positionatom[j, i] -
positionatom[mol1,
atom1])\)[\([1]\)]}, {fx \((positionatom[j, i] -
positionatom[mol1, atom1])\)[\([2]\)],
fy \((positionatom[j, i] -
positionatom[mol1, atom1])\)[\([2]\)],
fz \((positionatom[j, i] -
positionatom[mol1,
atom1])\)[\([2]\)]}, {fx \((positionatom[j, i] -
positionatom[mol1, atom1])\)[\([3]\)],
fy \((positionatom[j, i] -
positionatom[mol1, atom1])\)[\([3]\)],
fz \((positionatom[j, i] -
positionatom[mol1, atom1])\)[\([3]\)]}}], {j, 1,
Length[positions]}, {i, 1,
Length[positions[\([j]\)]]}]; {stress}]\), "\n",
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ElectrostaticStress[j, i], {j, 1, Length[positions]}, {i, 1,
Length[positions[\([j]\)]]}]/2.0,
1];\)\), "\[IndentingNewLine]",
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\(\(\(-\((\(StressTensor[\([1]\)]\)[\([1]\)] + \(StressTensor[\([2]\)]\)[\
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mol1)\) && \((i \[NotEqual] atom1)\))\),
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