Cleanup of some old issues with wrapper functions that obscured what …

…was going on.
RMGDFT · Jul 25, 2019 · b4d14b6 · b4d14b6
1 parent 856fee0
commit b4d14b6
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Showing 64 changed files with 111 additions and 356 deletions.
diff --git a/Headers/common_prototypes1.h b/Headers/common_prototypes1.h
@@ -209,7 +209,6 @@ int get_index (int gridpe, ION * iptr, int *Aix, int *Aiy, int *Aiz,
                int nxgrid, int nygrid, int nzgrid, double * xcstart, double * ycstart, double * zcstart);
 
 double linint (double *y, double rv, double invdr);
-void my_barrier (void);
 
 
 /* Conversion between crystal and cartesian coordinate prototypes */

diff --git a/Headers/rmg_control.h b/Headers/rmg_control.h
@@ -1,6 +1,6 @@
 #ifndef RMG_control_H
 #define RMG_control_H 1
-
+#include <vector>
 #include <stdbool.h>
 #ifdef __cplusplus
     #include <complex>

diff --git a/Misc/CMakeLists.txt b/Misc/CMakeLists.txt
@@ -77,7 +77,6 @@ get_index.c
 get_te.c
 minimage.c
 get_vtot_psi.c
-my_mpi.c
 blaswrappers.c
 set_bc.c
 cgen_prolong.c

diff --git a/NEGF/Common/InitNegf.cpp b/NEGF/Common/InitNegf.cpp
@@ -134,7 +134,7 @@ void InitNegf (double * vh, double * rho, double * rhocore, double * rhoc, doubl
 
     }                           /* endif */
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     /* Initialize the mehrstellen weights */
     /*get_mehr (); */
@@ -160,7 +160,7 @@ void InitNegf (double * vh, double * rho, double * rhocore, double * rhoc, doubl
     AllocatePsi (states, states1);
 
     duplicate_states_info (states, states1);
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
 
     pmo_init();
@@ -263,7 +263,7 @@ void InitNegf (double * vh, double * rho, double * rhocore, double * rhoc, doubl
 
 
     }
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
 
     for (level = 0; level < ct.eig_parm.levels + 1; level++)

diff --git a/NEGF/Common/Main.cpp b/NEGF/Common/Main.cpp
@@ -191,7 +191,7 @@ int main (int argc, char **argv)
     ReadOrbitals (ct.cfile, states, ct.ions, pct.img_comm, perm_ion_index);
     get_state_to_proc(states);
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     /*  Begin to do the real calculations */
     Run (states, states1, ControlMap);

diff --git a/NEGF/Common/QuenchNegf.cpp b/NEGF/Common/QuenchNegf.cpp
@@ -130,7 +130,7 @@ void QuenchNegf (STATE * states, STATE * states1, double * vxc, double * vh, dou
         sigma_all_energy_point (sigma_all, ct.kp[pct.kstart].kpt[1], ct.kp[pct.kstart].kpt[2]);
         delete(RT1);
     }
-    my_barrier();
+    MPI_Barrier(pct.img_comm);
     if(pct.imgpe==0) printf("\n sigma_all done");
 
 

diff --git a/NEGF/Common/Run.cpp b/NEGF/Common/Run.cpp
@@ -272,16 +272,16 @@ void Run (STATE * states, STATE * states1, std::unordered_map<std::string, Input
             write_data_lead (ct.outfile, vh, vxc, vh_old, vxc_old, rho);
 
 
-        my_barrier ();
+        MPI_Barrier(pct.img_comm);
         writeout_matrix_p ();
         delete(RT5);
 
-        my_barrier ();
+        MPI_Barrier(pct.img_comm);
         if (pct.imgpe == 0)
             printf ("\n Run done...\n");
         fflush (NULL);
 
-        my_barrier();
+        MPI_Barrier(pct.img_comm);
 
 
     }

diff --git a/NEGF/Common/ScfNegf.cpp b/NEGF/Common/ScfNegf.cpp
@@ -153,7 +153,7 @@ void ScfNegf (DoubleC *sigma_all, STATE * states, double *vxc,
     /* Generate new density */
     dcopy (&fpbasis, rho, &ione, rho_old, &ione);
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
     if (ct.runflag == 111 && ct.metal == 1)
         find_fermi (sigma_all);
     if (ct.runflag == 111 && ct.metal == 0)
@@ -165,13 +165,13 @@ void ScfNegf (DoubleC *sigma_all, STATE * states, double *vxc,
         delete(RT2);
     }
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     RmgTimer *RT3 = new RmgTimer("3-SCF: charge_density_matrix");
     charge_density_matrix_p (sigma_all);
 
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     delete(RT3);
 
@@ -235,7 +235,7 @@ void ScfNegf (DoubleC *sigma_all, STATE * states, double *vxc,
 
     /* mix_rho(rho, rho_old, ct.mix, ct.steps, 1); */
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     delete(RT5);
 
@@ -331,7 +331,7 @@ void update_pot (double *vxc, double *vh, double * vxc_old, double * vh_old, dou
         vtot[idx] = vxc[idx] + vh[idx] - vtot[idx];
     }
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     if (ct.scf_steps < 4 && ct.runflag == 0)
     {

diff --git a/NEGF/Common/allocate_matrix_LCR.c b/NEGF/Common/allocate_matrix_LCR.c
@@ -55,7 +55,7 @@ void allocate_matrix_LCR ()
 
 
     /* Wait until everybody gets here */
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     ntot = 0;
     ndim = 0;

diff --git a/NEGF/Common/apply_potential_drop.c b/NEGF/Common/apply_potential_drop.c
@@ -40,7 +40,7 @@ void apply_potential_drop (double *vbias)
     int x, y;
 
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     xoff = get_FPX_OFFSET();
     yoff = get_FPY_OFFSET();
@@ -411,7 +411,7 @@ void apply_potential_drop (double *vbias)
 
 
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
 
 }                              

diff --git a/NEGF/Common/get_3Ddos.c b/NEGF/Common/get_3Ddos.c
@@ -258,7 +258,7 @@ void get_3Ddos (STATE * states, double EMIN, double EMAX, int EPoints, int numbe
 			}
 		}
         }
-        my_barrier ();
+        MPI_Barrier(pct.img_comm);
     }
 
 
@@ -303,7 +303,7 @@ void get_3Ddos (STATE * states, double EMIN, double EMAX, int EPoints, int numbe
 	fclose (file);
     }
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
     fflush (NULL);
 
     /*===============================*/

diff --git a/NEGF/Common/get_cond_frommatrix.c b/NEGF/Common/get_cond_frommatrix.c
@@ -329,7 +329,7 @@ void get_cond_frommatrix ()
 
         }                           /*  end for iene */
 
-        my_barrier ();
+        MPI_Barrier(pct.img_comm);
         iene = E_POINTS;
         global_sums (cond, &iene, pct.grid_comm);
 
@@ -393,7 +393,7 @@ void get_cond_frommatrix ()
         my_free(lcr[iprobe].SCL);
     }
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
 }
 

diff --git a/NEGF/Common/get_cond_frommatrix_kyz.c b/NEGF/Common/get_cond_frommatrix_kyz.c
@@ -352,7 +352,7 @@ void get_cond_frommatrix_kyz ()
             } /*  end for iene */
 
 
-            my_barrier ();
+            MPI_Barrier(pct.img_comm);
 
             global_sums (cond_temp, &EP, pct.grid_comm);
 
@@ -499,7 +499,7 @@ void get_cond_frommatrix_kyz ()
         my_free(lcr[iprobe].SCL);
     }
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
 }
 

diff --git a/NEGF/Common/get_dos.c b/NEGF/Common/get_dos.c
@@ -294,7 +294,7 @@ void get_dos (STATE * states)
             }
         }
 
-        my_barrier ();
+        MPI_Barrier(pct.img_comm);
     }
 
 
@@ -354,7 +354,7 @@ void get_dos (STATE * states)
     }
 
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
     fflush (NULL);
 
     /*===============================*/

diff --git a/NEGF/Common/init_comp.c b/NEGF/Common/init_comp.c
@@ -50,7 +50,7 @@ void init_comp (double *vh)
 
     fflush(NULL);
 
-    my_barrier();
+    MPI_Barrier(pct.img_comm);
 
     /* Get this processors offset */
     pxoff = get_FPX_OFFSET();
@@ -159,7 +159,7 @@ void init_comp (double *vh)
 
     /* Wait until everyone gets here */
     fflush(NULL);
-    my_barrier();
+    MPI_Barrier(pct.img_comm);
     my_free(zvec);
 
 }                               /* end init_comp */

diff --git a/NEGF/Common/init_ext.c b/NEGF/Common/init_ext.c
@@ -40,7 +40,7 @@ void init_ext (double *vext, double gbias_begin, double gbias_end,  double BT, d
 
     fflush(NULL);
 
-    my_barrier();
+    MPI_Barrier(pct.img_comm);
 
 
     /* Grab some memory for storage */
@@ -89,7 +89,7 @@ void init_ext (double *vext, double gbias_begin, double gbias_end,  double BT, d
 
     /* Wait until everyone gets here */
     fflush(NULL);
-    my_barrier();
+    MPI_Barrier(pct.img_comm);
 
 }                               /* end init_ext */
 

diff --git a/NEGF/Common/init_loc_xyz.c b/NEGF/Common/init_loc_xyz.c
@@ -75,7 +75,7 @@ void init_loc_xyz ()
         printf ("\n init_loc_xyz.c  done\n");
 
     } 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
     fflush (NULL);
 
 

diff --git a/NEGF/Common/interpolation_orbit.c b/NEGF/Common/interpolation_orbit.c
@@ -213,7 +213,7 @@ lcr[idx0].x_shift);
     my_free(psi_old);
     my_free(psi_new);
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
     if (pct.gridpe == 0) printf ("\n interpolation_orbit  is done! ");
 
 }
diff --git a/NEGF/Common/lead_bandstructure.c b/NEGF/Common/lead_bandstructure.c
@@ -274,11 +274,11 @@ void lead_bandstructure ()
 
     }
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
     idx = kpoints[0] * nL;
     comm_sums (ener_band, &idx, COMM_EN1);
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
     if (pct.gridpe == 0)
     {
         file = fopen ("band.dat", "w");
@@ -294,6 +294,6 @@ void lead_bandstructure ()
             fprintf (file, "&\n");
         }
     }
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
 }
diff --git a/NEGF/Common/modify_rho.c b/NEGF/Common/modify_rho.c
@@ -171,7 +171,7 @@ void modify_rho (double * rho, double * rho_old)
          */
 
     }
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
 
 }
diff --git a/NEGF/Common/nlforce_partial_H_part2.c b/NEGF/Common/nlforce_partial_H_part2.c
@@ -230,7 +230,7 @@ void nlforce_partial_H_part2 (STATE * states, STATE * states1, double *GHG, doub
                 MPI_Send (psi1, size1, MPI_DOUBLE, proc1, i, pct.grid_comm);
             }
 
-        my_barrier ();
+        MPI_Barrier(pct.img_comm);
     }
 
 

diff --git a/NEGF/Common/partial_vloc.c b/NEGF/Common/partial_vloc.c
@@ -39,7 +39,7 @@ void partial_vloc ()
     SPECIES *sp;
 
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     /*  get total number of vnuc on this processor */
     /*  pct.n_ion_center: number of ions whose nl projector overlap
@@ -143,7 +143,7 @@ void partial_vloc ()
         printf (" partial_vloc.c  done\n");
 
     }
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
     fflush (NULL);
 
 }
diff --git a/NEGF/Common/pmo_init.c b/NEGF/Common/pmo_init.c
@@ -129,7 +129,7 @@ void pmo_init ()
     Cblacs_gridinfo (pmo.ictxt[pmo.myblacs], &nprow, &npcol, &myrow, &mycol);
 
     fflush(NULL);
-    my_barrier();
+    MPI_Barrier(pct.img_comm);
     /* If I'm not in the process grid, return */
     if(myrow == -1) return;
 

diff --git a/NEGF/Common/read_lead_matrix.c b/NEGF/Common/read_lead_matrix.c
@@ -49,7 +49,7 @@ void read_lead_matrix ()
     int size, rank, ndims, gsizes[2], distribs[2];
 
     /* Wait until everyone gets here */
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
 
     ictxt = pmo.ictxt[pmo.myblacs];

diff --git a/NEGF/Common/read_orbital.c b/NEGF/Common/read_orbital.c
@@ -43,7 +43,7 @@ void read_orbital (STATE * states)
 
 
     /* Wait until everybody gets here */
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
 /*
     printf ("state_begin, state_end %d %d \n", ct.state_begin, ct.state_end);
@@ -181,7 +181,7 @@ void read_orbital (STATE * states)
     }   /* st loop ends */
 
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     fflush (NULL);
 

diff --git a/NEGF/Common/read_potrho.c b/NEGF/Common/read_potrho.c
@@ -70,7 +70,7 @@ void read_potrho (double *vh, int iflag, char *file_ex)
 
 
     /* Wait until everybody gets here */
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     rcount = (int *) malloc(pct.grid_npes * sizeof(int));
     rdisp = (int *) malloc(pct.grid_npes * sizeof(int));
@@ -600,7 +600,7 @@ void read_potrho (double *vh, int iflag, char *file_ex)
 
 
 
-    my_barrier ();
+    MPI_Barrier(pct.img_comm);
 
     fflush (NULL);
-Original file line number
+Diff line change
@@ Expand Up / @@ -171,7 +171,7 @@ void modify_rho (double * rho, double * rho_old) @@
              */
         }
-        my_barrier ();
+        MPI_Barrier(pct.img_comm);
     }