Commit 1995f434 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

fix some more code formatting issues, add newline at EOF

parent db0281b4

src/USER-MISC/fix_filter_corotate.cpp

+62 −107
Original line number Diff line number Diff line
@@ -48,7 +48,7 @@ using namespace FixConst; 


// allocate space for static class variable



FixFilterCorotate *FixFilterCorotate::fsptr;

FixFilterCorotate *FixFilterCorotate::fsptr = NULL;



#define BIG 1.0e20

#define MASSDELTA 0.1
@@ -1259,29 +1259,6 @@ void FixFilterCorotate::find_clusters() 
  memory->destroy(partner_shake);

  memory->destroy(partner_nshake);



  // -----------------------------------------------------

  // set bond_type and angle_type negative for SHAKE clusters

  // must set for all SHAKE bonds and angles stored by each atom

  // -----------------------------------------------------



  /* for (i = 0; i < nlocal; i++) {

   *    if (shake_flag[i] == 0) continue;

   *    else if (shake_flag[i] == 1) {

   *      bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);

   *      bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],-1);

   *      angletype_findset(i,shake_atom[i][1],shake_atom[i][2],-1);

} else if (shake_flag[i] == 2) {

  bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);

} else if (shake_flag[i] == 3) {

  bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);

  bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],-1);

} else if (shake_flag[i] == 4) {

  bondtype_findset(i,shake_atom[i][0],shake_atom[i][1],-1);

  bondtype_findset(i,shake_atom[i][0],shake_atom[i][2],-1);

  bondtype_findset(i,shake_atom[i][0],shake_atom[i][3],-1);

}

}*/



  // -----------------------------------------------------

  // print info on SHAKE clusters

  // -----------------------------------------------------
@@ -1441,6 +1418,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
{

  //index: shake index, index_in_list: corresponding index in list

  //get q0, nselect:



  double *q0  = clist_q0[index_in_list];

  int nselect1  = clist_nselect1[index_in_list];

  int nselect2  = clist_nselect2[index_in_list];
@@ -1461,15 +1439,13 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
  for (int i = 0; i<N; i++)

    del[i] = new double[3];



  for (int i = 0; i < N; i++)

  {

  for (int i = 0; i < N; i++) {

    list_cluster[i] = atom->map(shake_atom[index][i]);

    m[i] = atom->mass[atom->type[list_cluster[i]]];

  }



  //%CALC r_i:

  for (int i = 1; i < N; i++)

  {

  for (int i = 1; i < N; i++) {

    del[i][0] = x[list_cluster[i]][0] - x[list_cluster[0]][0];

    del[i][1] = x[list_cluster[i]][1] - x[list_cluster[0]][1];

    del[i][2] = x[list_cluster[i]][2] - x[list_cluster[0]][2];
@@ -1484,8 +1460,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
  n1[0] = n1[1] = n1[2] = 0.0;



  int k;

  for (int i = 0; i < nselect1; i++)

  {

  for (int i = 0; i < nselect1; i++) {

    k = select1[i];

    n1[0] += del[k][0]*r[k];

    n1[1] += del[k][1]*r[k];
@@ -1500,8 +1475,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
  //calc n2:

  n2[0] = n2[1] = n2[2] = 0.0;



  for (int i = 0; i < nselect2; i++)

  {

  for (int i = 0; i < nselect2; i++) {

    k = select2[i];

    n2[0] += del[k][0]*r[k];

    n2[1] += del[k][1]*r[k];
@@ -1533,8 +1507,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
  n3[2] *= norm3;



  //%x_filter:

  for (int i = 0; i < N; i++)

  {

  for (int i = 0; i < N; i++) {

    k = list_cluster[i];

    array_atom[k][0] = x[k][0]+q0[3*i]*n1[0]+q0[3*i+1]*n2[0]+q0[3*i+2]*n3[0];

    array_atom[k][1] = x[k][1]+q0[3*i]*n1[1]+q0[3*i+1]*n2[1]+q0[3*i+2]*n3[1];
@@ -1547,11 +1520,9 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 


  //%x+X_center



  for (int i = 0; i<N; i++)

  {

  for (int i = 0; i<N; i++) {

    k = list_cluster[i];

    for (int j = 0; j < N; j++)

    {

    for (int j = 0; j < N; j++) {

      array_atom[k][0] += m[j]/m_all*(del[j][0]-del[i][0]);

      array_atom[k][1] += m[j]/m_all*(del[j][1]-del[i][1]);

      array_atom[k][2] += m[j]/m_all*(del[j][2]-del[i][2]);
@@ -1566,20 +1537,18 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
      sum1[i][j] = 0;



  double I3mn1n1T[3][3];   //(I_3 - n1n1T)

  for (int i=0; i<3; i++)

  {

  for (int i=0; i<3; i++) {

    for (int j=0; j<3; j++)

      I3mn1n1T[i][j] = -n1[i]*n1[j];

    I3mn1n1T[i][i] += 1.0;

  }



  // sum1 part of dn1dx:

  for (int l = 0; l < nselect1; l++)

  {



  for (int l = 0; l < nselect1; l++) {

    k = select1[l];

    for (int i=0; i<3; i++)

    {

      for (int j=0; j<3; j++)

      {

    for (int i=0; i<3; i++) {

      for (int j=0; j<3; j++) {

        double help = del[k][i]*del[k][j]*r[k]*r[k]*r[k];

        sum1[i][j+3*k] -= help;

        sum1[i][j] += help;
@@ -1588,11 +1557,11 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
      sum1[i][i] -= r[k];

    }

  }



  //dn1dx = norm1 * I3mn1n1T * sum1

  for (int i=0; i<3; i++)

  {

    for (int j=0; j<3*N; j++)

    {



  for (int i=0; i<3; i++) {

    for (int j=0; j<3*N; j++) {

      double sum = 0;

      for (int l = 0; l<3; l++)

        sum += I3mn1n1T[i][l]*sum1[l][j];
@@ -1601,27 +1570,25 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
  }



  //dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)



  double sum2[3][3*N];

  for (int i=0; i<3; i++)

    for (int j=0; j<3*N; j++)

      sum2[i][j] = 0;



  double I3mn2n2T[3][3];   //(I_3 - n2n2T)

  for (int i=0; i<3; i++)

  {

  for (int i=0; i<3; i++) {

    for (int j=0; j<3; j++)

      I3mn2n2T[i][j] = -n2[i]*n2[j];

    I3mn2n2T[i][i] += 1.0;

  }



  // sum2 part of dn1dx:

  for (int l = 0; l < nselect2; l++)

  {



  for (int l = 0; l < nselect2; l++) {

    k = select2[l];

    for (int i=0; i<3; i++)

    {

      for (int j=0; j<3; j++)

      {

    for (int i=0; i<3; i++) {

      for (int j=0; j<3; j++) {

        double help = del[k][i]*del[k][j]*r[k]*r[k]*r[k];

        sum2[i][j+3*k] -= help;

        sum2[i][j] += help;
@@ -1631,54 +1598,51 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
    }

  }



  //prefaktor:

  //prefactor:



  double rkn1pn1rk[3][3];

  double rk[3]; rk[0] = rk[1] = rk[2] = 0.0;



  for (int i = 0; i < nselect2; i++)

  {

  for (int i = 0; i < nselect2; i++) {

    k = select2[i];

    rk[0] += del[k][0]*r[k];

    rk[1] += del[k][1]*r[k];

    rk[2] += del[k][2]*r[k];

  }



  //rkn1pn1rk = rkT*n1*I3 + n1*rkT



  double scalar = rk[0]*n1[0]+rk[1]*n1[1]+rk[2]*n1[2];

  for (int i=0; i<3; i++)

  {

  for (int i=0; i<3; i++) {

    for (int j=0; j<3; j++)

      rkn1pn1rk[i][j] = n1[i]*rk[j];

    rkn1pn1rk[i][i] += scalar;

  }



  //dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)

  //sum3 = (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)



  double sum3[3][3*N];

  for (int i=0; i<3; i++)

  {

    for (int j=0; j<3*N; j++)

    {

    for (int j=0; j<3*N; j++) {

      double sum = 0;

      for (int l = 0; l<3; l++)

        sum += I3mn1n1T[i][l]*sum2[l][j] - rkn1pn1rk[i][l]*dn1dx[l][j];

      sum3[i][j] = sum;

    }

  }



  //dn2dx = norm2 * I3mn2n2T * sum3

  for (int i=0; i<3; i++)

  {

    for (int j=0; j<3*N; j++)

    {

    for (int j=0; j<3*N; j++) {

      double sum = 0;

      for (int l = 0; l<3; l++)

        sum += I3mn2n2T[i][l]*sum3[l][j];

      dn2dx[i][j] = norm2*sum;

    }

  }



  //dn3dx = norm3 * I3mn3n3T * cross

  double I3mn3n3T[3][3];   //(I_3 - n3n3T)

  for (int i=0; i<3; i++)

  {

  for (int i=0; i<3; i++) {

    for (int j=0; j<3; j++)

      I3mn3n3T[i][j] = -n3[i]*n3[j];

    I3mn3n3T[i][i] += 1.0;
@@ -1686,8 +1650,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 


  double cross[3][3*N];



  for (int j=0; j<3*N; j++)

  {

  for (int j=0; j<3*N; j++) {

    cross[0][j] = dn1dx[1][j]*n2[2] -dn1dx[2][j]*n2[1] +

      n1[1]*dn2dx[2][j]-n1[2]*dn2dx[1][j];

    cross[1][j] = dn1dx[2][j]*n2[0] -dn1dx[0][j]*n2[2] +
@@ -1697,15 +1660,12 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list) 
  }



  for (int i=0; i<3; i++)

  {

    for (int j=0; j<3*N; j++)

    {

    for (int j=0; j<3*N; j++) {

      double sum = 0;

      for (int l = 0; l<3; l++)

        sum += I3mn3n3T[i][l]*cross[l][j];

      dn3dx[i][j] = norm3*sum;

    }

  }



  for (int l=0; l<N; l++)

    for (int i=0; i<3; i++)
@@ -1738,8 +1698,7 @@ int FixFilterCorotate::pack_forward_comm(int n, int *list, double *buf, 
  int i,j,m;

  double**f = atom->f;

  m = 0;

  for (i = 0; i < n; i++)

  {

  for (i = 0; i < n; i++) {

    j = list[i];



    buf[m++] = f[j][0];
@@ -1866,10 +1825,6 @@ double FixFilterCorotate::memory_usage() 
  bytes += (nb+na+nt)*sizeof(int);

  bytes += (nt-1+nb+na+15*15+18+10*15)*sizeof(double);



  //output:

  //bytes += (2*nb+2*na)*sizeof(int);

  //bytes += (6*na+6*nb)*sizeof(double);



  return bytes;

}

src/USER-MISC/fix_filter_corotate.h

+1 −1

File changed.

Contains only whitespace changes.

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