Aspects of the alloy app and scripts

1. Program

1. 我在constructor和header file加了member variables (原本app_diffusion是有的 )

//app_alloy.cpp
//1. Delete all things about Shweobel Hop
  // statistics
  ndeposit = ndep_failed = 0;
  nhop = 0;
//app_alloy.cpp
int ndeposit, ndep_failed, nhop;
double **Q;
double **hbarrier
int particleid //a global variable

2. 大部分的array还需要一个alloc method，注意在deconstructor里也加上新的allocated memory

//cpp line 704 allocate_data()
// creat() alloc memory for 2D arrays, they NEED to be initialized!
  memory->create(firstevent,nlocal,"app:firstevent");
  memory->create(hbarrier,maxneigh+1,maxneigh+1,"app:hbarrier");
  for (int i = 0; i <= maxneigh; i++)
    for (int j = 0; j <= maxneigh; j++)
      hbarrier[i][j]  = 0.0;
      
  memory->create(Q, 128, 128, "app:Q");
  for (int i = 0; i < 128; i++)
    for (int j = 0; j < 128; j++)
      Q[i][j] = 0.0;
      
  hopsite = new int[maxneigh*maxneigh + maxneigh];
  
//cpp line 27 Alloy constructor for other initializations
//pointers are all instantiated as nullptr, in C style NULL  
  ninteger = 2; ndouble = 0;
  delpropensity = 3; delevent = 1;
  allow_kmc = 1;
  create_arrays();
  maxevent = 0;
  events = NULL; firstevent = NULL;
  Q = NULL;
  particleid = 0;
  hbarrier = NULL;
  //ecoord = NULL;
  hopsite = NULL;
  
//cpp line 73 AppAlloy::~AppAlloy() deconstructor
  memory->sfree(events);
  memory->destroy(firstevent);
  //delete Q, Q[128][128]
  memory->destroy(Q);
  memory->destroy(hbarrier);
  //delete [] ecoord;
  delete [] hopsite;

3.在 input_app() 可以添加和修改command, 比如说deposition里加了一个particleid, 注意这个是global variable, 需要在header file 里面declare. 有点类似于C0 virtual machine，可以定制command。

  if (strcmp(command,"deposition") == 0) {
   
    if (narg < 1) error->all(FLERR,"Illegal deposition command");
    if (strcmp(arg[0],