Merge pull request #1177 from lammps/modify-reorder

  restart_deallocate(1);

  // init each compute

  // set invoked_scalar,vector,etc to -1 to force new run to re-compute them

  // add initial timestep to all computes that store invocation times

  //   since any of them may be invoked by initial thermo

  // do not clear out invocation times stored within a compute,

  //   b/c some may be holdovers from previous run, like for ave fixes

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

    compute[i]->init();

    compute[i]->invoked_scalar = -1;

    compute[i]->invoked_vector = -1;

    compute[i]->invoked_array = -1;

    compute[i]->invoked_peratom = -1;

    compute[i]->invoked_local = -1;

  }

  addstep_compute_all(update->ntimestep);

  // init each fix

  // should not need to come before compute init

  //   used to b/c temperature computes called fix->dof() in their init,

  //   and fix rigid required its own init before its dof() could be called,

  //   but computes now do their DOF in setup()

  for (i = 0; i < nfix; i++) fix[i]->init();

  // set global flag if any fix has its restart_pbc flag set

  restart_pbc_any = 0;

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

    if (fix[i]->restart_pbc) restart_pbc_any = 1;

  // create lists of fixes to call at each stage of run

  // needs to happen after init() of computes

  //   b/c a compute::init() can delete a fix, e.g. compute chunk/atom

  list_init(INITIAL_INTEGRATE,n_initial_integrate,list_initial_integrate);

  list_init(POST_INTEGRATE,n_post_integrate,list_post_integrate);

  list_init(MIN_POST_FORCE,n_min_post_force,list_min_post_force);

  list_init(MIN_ENERGY,n_min_energy,list_min_energy);

  // init each fix

  // not sure if now needs to come before compute init

  // used to b/c temperature computes called fix->dof() in their init,

  // and fix rigid required its own init before its dof() could be called,

  // but computes now do their DOF in setup()

  for (i = 0; i < nfix; i++) fix[i]->init();

  // set global flag if any fix has its restart_pbc flag set

  restart_pbc_any = 0;

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

    if (fix[i]->restart_pbc) restart_pbc_any = 1;

  // create list of computes that store invocation times

  list_init_compute();

  // init each compute

  // set invoked_scalar,vector,etc to -1 to force new run to re-compute them

  // add initial timestep to all computes that store invocation times

  //   since any of them may be invoked by initial thermo

  // do not clear out invocation times stored within a compute,

  //   b/c some may be holdovers from previous run, like for ave fixes

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

    compute[i]->init();

    compute[i]->invoked_scalar = -1;

    compute[i]->invoked_vector = -1;

    compute[i]->invoked_array = -1;

    compute[i]->invoked_peratom = -1;

    compute[i]->invoked_local = -1;

  }

  addstep_compute_all(update->ntimestep);

  // error if any fix or compute is using a dynamic group when not allowed

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

    if (!compute[i]->dynamic_group_allow &&

        group->dynamic[compute[i]->igroup]) {

      char str[128];

      snprintf(str,128,"Compute %s does not allow use of dynamic group",fix[i]->id);

      snprintf(str,128,"Compute %s does not allow use of dynamic group",

               fix[i]->id);

      error->all(FLERR,str);

    }