LammpsFileManipulation/AtomClass.cpp at master · DeepChoudhuri/LammpsFileManipulation · GitHub

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
#include<iostream>

#include "AtomClass.h"
#include <cmath>

AtomClass::AtomClass()
{
  this->sij = new double[8];
  this->delSij = new double[8];

  this->setZeros();
}

// Sets up all variables i.e. per-atom quantities to zero
void AtomClass::setZeros()
{
  this->id = 0;
  this->type = 0;

  this->xpos = 0.0;
  this->ypos = 0.0;
  this->zpos = 0.0;

  this->vol = 0.0;
  this->csym = 0.0;
  this->pe = 0.0;

  for(int i = 0; i < 8; ++i)
  {
    this->sij[i] = 0.0;
    this->delSij[i] = 0.0;
  }
}


// each row of per-atom data is saved in the variables defined in the atom class
void AtomClass::readAtomValues(int itemNumbers, std::string *itemList, std::string *atomInfo)
{
  for(int i = 2; i < itemNumbers + 2 ; i++)
  {
    try{
        //std::cout<< itemList[i] << " " << atomInfo[i-2] << std::endl;
        if(itemList[i].compare("id")==0)
          this->id = std::stoi(atomInfo[i-2]);

        if(itemList[i].compare("type")==0)
          this->type = std::stoi(atomInfo[i-2]);

        if(itemList[i].compare("x")==0)
          this->xpos = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("y")==0)
          this->ypos = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("z")==0)
          this->zpos = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("v_volatm")==0)
          this->vol = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("c_csym")==0)
          this->csym = std::stod(atomInfo[i-2]);

        //if(itemList[i].compare("c_peatm")==0){
        if(itemList[i].compare("c_peratom")==0){
          this->pe = std::stod(atomInfo[i-2]);
          //std::cout<< itemList[i] <<" pe debug"<< this->pe << " " << atomInfo[i-2] << std::endl;
        }

        if(itemList[i].compare("v_s11")==0)
          this->sij[0] = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("v_s22")==0)
          this->sij[1] = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("v_s33")==0)
          this->sij[2] = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("v_s12")==0)
          this->sij[3] = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("v_s23")==0)
          this->sij[4] = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("v_s31")==0)
          this->sij[5] = std::stod(atomInfo[i-2]);

        if(itemList[i].compare("v_sii")==0)
          this->sij[6] = this->meanStress(this->sij[0], this->sij[1], this->sij[2]);

        //if(itemList[i].compare("v_svm")==0){
          //std::cout<< itemList[i] <<" debug"<< std::endl;
          this->sij[7] = this->vonMisses(this->sij[0], this->sij[1], this->sij[2], this->sij[3], this->sij[4], this->sij[5]);
         //}
        }
     catch(std::exception e)
     {
       std::cout << "Bad string! Error in string to integer/double conversion" << std::endl;
       std::cout << "Error with " << itemList[i] << ", string-value  = " << atomInfo[i-2] <<std::endl;
     }
  }
}


// Write all atom data  on the screen for debugging
void AtomClass::writeAtomData()
{
  std::cout << "id " <<  this->id << std::endl;
  std::cout << "type " << this->type << std::endl;
  std::cout << "xs " << this->xpos << std::endl;
  std::cout << "ys " << this->ypos << std::endl;
  std::cout << "xs " << this->zpos << std::endl;
  std::cout << "v_volatm " << this->vol << std::endl;
  std::cout << "c_csym " << this->csym << std::endl;
  std::cout << "c_peatm " << this->pe << std::endl;
  std::cout << "v_s11 " << this->sij[0] << std::endl;
  std::cout << "v_s22 " << this->sij[1] << std::endl;
  std::cout << "v_s33 " << this->sij[2] << std::endl;
  std::cout << "v_s12 " << this->sij[3] << std::endl;
  std::cout << "v_s23 " << this->sij[4] << std::endl;
  std::cout << "v_s31 " << this->sij[5] << std::endl;
  std::cout << "v_sii " << this->sij[6] << std::endl;
  std::cout << "v_svm " << this->sij[7] << std::endl;
  std::cout << "v_dels11 " << this->delSij[0] << std::endl;
  std::cout << "v_dels22 " << this->delSij[1] << std::endl;
  std::cout << "v_dels33 " << this->delSij[2] << std::endl;
  std::cout << "v_dels12 " << this->delSij[3] << std::endl;
  std::cout << "v_dels23 " << this->delSij[4] << std::endl;
  std::cout << "v_dels31 " << this->delSij[5] << std::endl;
  std::cout << "v_delsii " << this->delSij[6] << std::endl;
  std::cout << "v_delsvm " << this->delSij[7] << std::endl;
}


double AtomClass::vonMisses(double s11, double s22, double s33, double s12, double s23, double s31)
{
  double val = 0.0;

  val = std::sqrt((1.0/2.0)*(std::pow((s11 - s22),2.0) + std::pow((s22 - s33),2.0) + \
        std::pow((s33 - s11),2.0) + 6.0*(std::pow(s12,2.0) + std::pow(s23,2.0) + std::pow(s31,2.0))));
  //std::cout << "Val = " << val << std::endl;

  return val;
}


double AtomClass::meanStress(double s11, double s22, double s33)
{
  return (1.0/3.0)*(s11 + s22 + s33);
}


AtomClass::~AtomClass()
{
  delete []this->sij;
  delete []this->delSij;
}