lammps-sys 0.6.0

Generates bindings to LAMMPS' C interface (with optional builds from source)
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186

#include "WeakEquationElectronMomentum.h"
#include "Material.h"
#include "LammpsInterface.h"

namespace ATC {

//==============================================================
//  Class WeakEquationElectronMomentum
//==============================================================

//--------------------------------------------------------------
//  Constructor
//--------------------------------------------------------------
WeakEquationElectronMomentum::WeakEquationElectronMomentum()
  : WeakEquation(STATIC_PDE,ELECTRON_VELOCITY,3)
{}

//--------------------------------------------------------------
//  Destructor
//--------------------------------------------------------------
WeakEquationElectronMomentum::~WeakEquationElectronMomentum()
{}

void WeakEquationElectronMomentum::convection(const FIELD_MATS &fields,
                                              const Material * material,
                                              DENS_MAT_VEC & flux) const
{
  // set up mass density
  FIELD_MATS::const_iterator nField = fields.find(ELECTRON_DENSITY);
  const DENS_MAT & n = nField->second;
  DENS_MAT nMe(n.nRows(),n.nCols()); 
  material->inv_effective_mass(fields,nMe);
  nMe = n.div_by_element(nMe);

  // set up velocity and flux
  FIELD_MATS::const_iterator vField = fields.find(ELECTRON_VELOCITY);
  const DENS_MAT & velocity = vField->second;
  const CLON_VEC u(velocity,CLONE_COL,0);
  const CLON_VEC v(velocity,CLONE_COL,1);
  const CLON_VEC w(velocity,CLONE_COL,2);
  flux[0] = velocity; 
  flux[1] = velocity;
  flux[2] = velocity;
  CLON_VEC nuu(flux[0],CLONE_COL,0);
  CLON_VEC nuv(flux[1],CLONE_COL,0);
  CLON_VEC nuw(flux[2],CLONE_COL,0);
  CLON_VEC nvu(flux[0],CLONE_COL,1);
  CLON_VEC nvv(flux[1],CLONE_COL,1);
  CLON_VEC nvw(flux[2],CLONE_COL,1);
  CLON_VEC nwu(flux[0],CLONE_COL,2);
  CLON_VEC nwv(flux[1],CLONE_COL,2);
  CLON_VEC nww(flux[2],CLONE_COL,2);
  
  for (int i = 0; i < n.nRows(); i++) {
    // tensor product of velocities
    nuu(i) *= nMe(i,0)*u(i);
    nuv(i) *= nMe(i,0)*v(i);
    nuw(i) *= nMe(i,0)*w(i);
    nvu(i) *= nMe(i,0)*u(i);
    nvv(i) *= nMe(i,0)*v(i);
    nvw(i) *= nMe(i,0)*w(i);
    nwu(i) *= nMe(i,0)*u(i);
    nwv(i) *= nMe(i,0)*v(i);
    nww(i) *= nMe(i,0)*w(i);
  }
};

//---------------------------------------------------------------------
//   compute mass density
//---------------------------------------------------------------------
void WeakEquationElectronMomentum::M_integrand(
  const FIELD_MATS &fields,
  const Material * material,
  DENS_MAT & density ) const
{
  material->electron_mass_density(fields, density);
}

//--------------------------------------------------------------
void WeakEquationElectronMomentum::B_integrand(
  const FIELD_MATS &fields,
  const GRAD_FIELD_MATS &grad_fields,
  const Material * material,
  DENS_MAT_VEC &flux) const
{
  convection(fields,material,flux);
}

//==============================================================
//  Class WeakEquationElectronMomentumDDM
//==============================================================

//--------------------------------------------------------------
//  Constructor
//--------------------------------------------------------------
WeakEquationElectronMomentumDDM::WeakEquationElectronMomentumDDM()
  : WeakEquationElectronMomentum()
{
  DENS_MAT dummy;
  _dnCp_.reserve(nsd_);
  for (int i = 0; i < nsd_; i++)
    _dnCp_.push_back(dummy);

  _electricForce_.reserve(nsd_);
  for (int i = 0; i < nsd_; i++)
    _electricForce_.push_back(dummy);
}

//--------------------------------------------------------------
//  Destructor
//--------------------------------------------------------------
WeakEquationElectronMomentumDDM::~WeakEquationElectronMomentumDDM()
{}

void WeakEquationElectronMomentumDDM::thermal_stress(const FIELD_MATS &fields,
                                                     const GRAD_FIELD_MATS &gradFields,
                                                     const Material * material,
                                                     DENS_MAT &flux) const
{
  GRAD_FIELD_MATS::const_iterator dtField = gradFields.find(ELECTRON_TEMPERATURE);
  const DENS_MAT_VEC & DTe = dtField->second;

  CLON_VEC tsx(flux,CLONE_COL,0);
  CLON_VEC tsy(flux,CLONE_COL,1);
  CLON_VEC tsz(flux,CLONE_COL,2);

  // ith velocity component has thermal stress of
  // d_i n * Cp * Te
  DENS_MAT nCp(DTe[0].nRows(),DTe[0].nCols());  
  material->electron_heat_capacity(fields,nCp);
  nCp *= 2./3.;  // correction to capacity account for convection
  
  tsx += nCp.mult_by_element(DTe[0]);
  tsy += nCp.mult_by_element(DTe[1]);
  tsz += nCp.mult_by_element(DTe[2]);
  
  FIELD_MATS::const_iterator tField = fields.find(ELECTRON_TEMPERATURE);
  const DENS_MAT & Te = tField->second;
  
  material->D_electron_heat_capacity(fields,gradFields,_dnCp_);
  for (int i = 0; i < nsd_; i++)
    _dnCp_[i] *= 2./3.; // correction to capacity account for convection
  tsx += Te.mult_by_element(_dnCp_[0]);
  tsy += Te.mult_by_element(_dnCp_[1]);
  tsz += Te.mult_by_element(_dnCp_[2]);
}

//---------------------------------------------------------------------
//   compute mass density
//---------------------------------------------------------------------
void WeakEquationElectronMomentumDDM::M_integrand(
  const FIELD_MATS &fields,
  const Material * material,
  DENS_MAT & density ) const
{
  material->electron_drag_velocity_coefficient(fields, density);
}

//--------------------------------------------------------------
bool WeakEquationElectronMomentumDDM::N_integrand(
  const FIELD_MATS &fields,
  const GRAD_FIELD_MATS &grad_fields,
  const Material * material,
  DENS_MAT &flux) const
{
  FIELD_MATS::const_iterator vField = fields.find(ELECTRON_VELOCITY);
  const DENS_MAT & velocity = vField->second;
  flux.reset(velocity.nRows(),velocity.nCols());
  thermal_stress(fields, grad_fields, material, flux);
  material->electric_displacement(fields, grad_fields, _electricForce_);


  FIELD_MATS::const_iterator nField = fields.find(ELECTRON_DENSITY);
  const DENS_MAT & n = nField->second;

  
  CLON_VEC tsx(flux,CLONE_COL,0);
  CLON_VEC tsy(flux,CLONE_COL,1);
  CLON_VEC tsz(flux,CLONE_COL,2);
  tsx += n.mult_by_element(_electricForce_[0]);
  tsy += n.mult_by_element(_electricForce_[1]);
  tsz += n.mult_by_element(_electricForce_[2]);
  return true;
}

}; // END namespace