Merge branch 'master' into more-fmtlib-use

   \sigma_i  = & \sum_{j=i_1}^{i_N} q_j \cdot \psi_{ij} \left(r_{ij}\right) \\

   E_i\left(q_i,\sigma_i\right)  = & \frac{1}{2} \cdot q_i \cdot \sigma_i

where :math:`\eta_{ji} is a pairwise function describing electron flow from atom

where :math:`\eta_{ji}` is a pairwise function describing electron flow from atom

I to atom J, and :math:`\psi_{ij}` is another pairwise function.  The multi-body

nature of the EIM potential is a result of the embedding energy term.

A complete list of all the pair functions used in EIM is summarized

   \right.\\

   \eta_{ji} = & A_{\eta,ij}\left(\chi_j-\chi_i\right)f_c\left(r,r_{s,\eta,ij},r_{c,\eta,ij}\right) \\

   \psi_{ij}\left(r\right) = & A_{\psi,ij}\exp\left(-\zeta_{ij}r\right)f_c\left(r,r_{s,\psi,ij},r_{c,\psi,ij}\right) \\

   f_{c}\left(r,r_p,r_c\right) = & 0.510204 \mathrm{erfc}\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204

   f_{c}\left(r,r_p,r_c\right) = & 0.510204 \cdot \mathrm{erfc}\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204

Here :math:`E_b, r_e, r_(c,\phi), \alpha, \beta, A_(\psi), \zeta, r_(s,\psi),

r_(c,\psi), A_(\eta), r_(s,\eta), r_(c,\eta), \chi,` and pair function type

# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber,  Phys Rev B, 31, 5262, (1985)

# Stillinger-Weber parameters for various elements and mixtures

# multiple entries can be added to this file, LAMMPS reads the ones it needs

# these entries are in LAMMPS "metal" units:

#   epsilon = eV; sigma = Angstroms

#   other quantities are unitless

# format of a single entry (one or more lines):

#   element 1, element 2, element 3, 

#   epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol

# Here are the original parameters in metal units, for Silicon from:

#

# Stillinger and Weber,  Phys. Rev. B, v. 31, p. 5262, (1985)

#

Si Si Si 2.1683  2.0951  1.80  21.0  1.20  -0.333333333333

         7.049556277  0.6022245584  4.0  0.0 0.0

../../potentials/Si.sw

 No newline at end of file

# DATE: 2016-07-29 UNITS: metal CONTRIBUTOR: Todd Zeitler, tzeitle@sandia.gov CITATION: none 

# DATE: 2016-07-29 UNITS: real CONTRIBUTOR: Todd Zeitler, tzeitle@sandia.gov CITATION: none

# nb3b/harmonic (nonbonded 3-body harmonic) parameters for various elements

#

# multiple entries can be added to this file, LAMMPS reads the ones it needs

#include "fix_nph_asphere.h"

#include <cstring>

#include <string>

#include "modify.h"

#include "error.h"

  // compute group = all since pressure is always global (group all)

  // and thus its KE/temperature contribution should use group all

  int n = strlen(id) + 6;

  id_temp = new char[n];

  strcpy(id_temp,id);

  strcat(id_temp,"_temp");

  std::string tcmd = id + std::string("_temp");

  id_temp = new char[tcmd.size()+1];

  strcpy(id_temp,tcmd.c_str());

  char **newarg = new char*[3];

  newarg[0] = id_temp;

  newarg[1] = (char *) "all";

  newarg[2] = (char *) "temp/asphere";

  modify->add_compute(3,newarg);

  delete [] newarg;

  modify->add_compute(tcmd + " all temp/asphere");

  tcomputeflag = 1;

  // create a new compute pressure style

  // id = fix-ID + press, compute group = all

  // pass id_temp as 4th arg to pressure constructor

  n = strlen(id) + 7;

  id_press = new char[n];

  strcpy(id_press,id);

  strcat(id_press,"_press");

  std::string pcmd = id + std::string("_press");

  id_press = new char[pcmd.size()+1];

  strcpy(id_press,pcmd.c_str());

  newarg = new char*[4];

  newarg[0] = id_press;

  newarg[1] = (char *) "all";

  newarg[2] = (char *) "pressure";

  newarg[3] = id_temp;

  modify->add_compute(4,newarg);

  delete [] newarg;

  modify->add_compute(pcmd + " all pressure " + std::string(id_temp));

  pcomputeflag = 1;

}