Start new energy calculation from where it stopped

[mboaks]

Hi,

I am a new abinit user. I am trying to calculate total energy of silicon supercell containing 4 conventional unit cells in x,y,z directions and 1/4 th of a pore (pore radius = 15 Angstrom). I ran the simulation in available supercomputer facility at the university but it ran out of wall time after 16 iterations.Is there any way to resume the simulation from where it stopped? Please suggest. My input was as follows:

Please feel free to suggest if there is any way I can expedite the simulation.

# Crystalline silicon : computation of the total energy for 4x4x4 Si super cell
#

#Definition of the unit cell
acell 5.43070 5.43070 5.43070 Angstr #
rprim 4 0 0 # In lessons 1 and 2, these primitive vectors
0 4 0 # (to be scaled by acell) were 1 0 0 0 1 0 0 0 1
0 0 4 # that is, the default.
chkprim 0

#Definition of the atom types
ntypat 1 # There is only one type of atom
znucl 14 # The keyword "znucl" refers to the atomic number of the
# possible type(s) of atom. The pseudopotential(s)
# mentioned in the "files" file must correspond
# to the type(s) of atom. Here, the only type is Silicon.

chksymbreak 0
#Definition of the atoms
natom 512 # There are 512 atoms
typat 512*1 # All 512 atoms are of type 1, that is, Silicon.
xangst # This keyword indicate that the location of the atoms
# will follow, one triplet of number for each atom
0.00000 0.00000 0.00000
0.00000 2.71535 2.71535
2.71535 2.71535 0.00000
2.71535 0.00000 2.71535
4.07302 1.35767 4.07302
1.35767 1.35767 1.35767
1.35767 4.07302 4.07302
4.07302 4.07302 1.35767
0.00000 0.00000 5.43070
0.00000 2.71535 8.14605
2.71535 2.71535 5.43070
2.71535 0.00000 8.14605
4.07302 1.35767 9.50372
1.35767 1.35767 6.78837
1.35767 4.07302 9.50372
4.07302 4.07302 6.78837
0.00000 0.00000 10.86140
0.00000 2.71535 13.57675
2.71535 2.71535 10.86140
2.71535 0.00000 13.57675
4.07302 1.35767 14.93442
1.35767 1.35767 12.21907
1.35767 4.07302 14.93442
4.07302 4.07302 12.21907
0.00000 0.00000 16.29210
0.00000 2.71535 19.00745
2.71535 2.71535 16.29210
2.71535 0.00000 19.00745
4.07302 1.35767 20.36512
1.35767 1.35767 17.64977
1.35767 4.07302 20.36512
4.07302 4.07302 17.64977
0.00000 5.43070 0.00000
0.00000 8.14605 2.71535
2.71535 8.14605 0.00000
2.71535 5.43070 2.71535
4.07302 6.78837 4.07302
1.35767 6.78837 1.35767
1.35767 9.50372 4.07302
4.07302 9.50372 1.35767
0.00000 5.43070 5.43070
0.00000 8.14605 8.14605
2.71535 8.14605 5.43070
2.71535 5.43070 8.14605
4.07302 6.78837 9.50372
1.35767 6.78837 6.78837
1.35767 9.50372 9.50372
4.07302 9.50372 6.78837
0.00000 5.43070 10.86140
0.00000 8.14605 13.57675
2.71535 8.14605 10.86140
2.71535 5.43070 13.57675
4.07302 6.78837 14.93442
1.35767 6.78837 12.21907
1.35767 9.50372 14.93442
4.07302 9.50372 12.21907
0.00000 5.43070 16.29210
0.00000 8.14605 19.00745
2.71535 8.14605 16.29210
2.71535 5.43070 19.00745
4.07302 6.78837 20.36512
1.35767 6.78837 17.64977
1.35767 9.50372 20.36512
4.07302 9.50372 17.64977
0.00000 10.86140 0.00000
0.00000 13.57675 2.71535
2.71535 13.57675 0.00000
2.71535 10.86140 2.71535
4.07302 12.21907 4.07302
1.35767 12.21907 1.35767
1.35767 14.93442 4.07302
4.07302 14.93442 1.35767
0.00000 10.86140 5.43070
0.00000 13.57675 8.14605
2.71535 13.57675 5.43070
2.71535 10.86140 8.14605
4.07302 12.21907 9.50372
1.35767 12.21907 6.78837
1.35767 14.93442 9.50372
4.07302 14.93442 6.78837
0.00000 10.86140 10.86140
0.00000 13.57675 13.57675
2.71535 13.57675 10.86140
2.71535 10.86140 13.57675
4.07302 12.21907 14.93442
1.35767 12.21907 12.21907
1.35767 14.93442 14.93442
4.07302 14.93442 12.21907
0.00000 10.86140 16.29210
0.00000 13.57675 19.00745
2.71535 13.57675 16.29210
2.71535 10.86140 19.00745
4.07302 12.21907 20.36512
1.35767 12.21907 17.64977
1.35767 14.93442 20.36512
4.07302 14.93442 17.64977
0.00000 16.29210 0.00000
0.00000 19.00745 2.71535
2.71535 19.00745 0.00000
2.71535 16.29210 2.71535
4.07302 17.64977 4.07302
1.35767 17.64977 1.35767
1.35767 20.36512 4.07302
4.07302 20.36512 1.35767
0.00000 16.29210 5.43070
0.00000 19.00745 8.14605
2.71535 19.00745 5.43070
2.71535 16.29210 8.14605
4.07302 17.64977 9.50372
1.35767 17.64977 6.78837
1.35767 20.36512 9.50372
4.07302 20.36512 6.78837
0.00000 16.29210 10.86140
0.00000 19.00745 13.57675
2.71535 19.00745 10.86140
2.71535 16.29210 13.57675
4.07302 17.64977 14.93442
1.35767 17.64977 12.21907
1.35767 20.36512 14.93442
4.07302 20.36512 12.21907
0.00000 16.29210 16.29210
0.00000 19.00745 19.00745
2.71535 19.00745 16.29210
2.71535 16.29210 19.00745
4.07302 17.64977 20.36512
1.35767 17.64977 17.64977
1.35767 20.36512 20.36512
4.07302 20.36512 17.64977
5.43070 0.00000 0.00000
5.43070 2.71535 2.71535
8.14605 2.71535 0.00000
8.14605 0.00000 2.71535
9.50372 1.35767 4.07302
6.78837 1.35767 1.35767
6.78837 4.07302 4.07302
9.50372 4.07302 1.35767
5.43070 0.00000 5.43070
5.43070 2.71535 8.14605
8.14605 2.71535 5.43070
8.14605 0.00000 8.14605
9.50372 1.35767 9.50372
6.78837 1.35767 6.78837
6.78837 4.07302 9.50372
9.50372 4.07302 6.78837
5.43070 0.00000 10.86140
5.43070 2.71535 13.57675
8.14605 2.71535 10.86140
8.14605 0.00000 13.57675
9.50372 1.35767 14.93442
6.78837 1.35767 12.21907
6.78837 4.07302 14.93442
9.50372 4.07302 12.21907
5.43070 0.00000 16.29210
5.43070 2.71535 19.00745
8.14605 2.71535 16.29210
8.14605 0.00000 19.00745
9.50372 1.35767 20.36512
6.78837 1.35767 17.64977
6.78837 4.07302 20.36512
9.50372 4.07302 17.64977
5.43070 5.43070 0.00000
5.43070 8.14605 2.71535
8.14605 8.14605 0.00000
8.14605 5.43070 2.71535
9.50372 6.78837 4.07302
6.78837 6.78837 1.35767
6.78837 9.50372 4.07302
9.50372 9.50372 1.35767
5.43070 5.43070 5.43070
5.43070 8.14605 8.14605
8.14605 8.14605 5.43070
8.14605 5.43070 8.14605
9.50372 6.78837 9.50372
6.78837 6.78837 6.78837
6.78837 9.50372 9.50372
9.50372 9.50372 6.78837
5.43070 5.43070 10.86140
5.43070 8.14605 13.57675
8.14605 8.14605 10.86140
8.14605 5.43070 13.57675
9.50372 6.78837 14.93442
6.78837 6.78837 12.21907
6.78837 9.50372 14.93442
9.50372 9.50372 12.21907
5.43070 5.43070 16.29210
5.43070 8.14605 19.00745
8.14605 8.14605 16.29210
8.14605 5.43070 19.00745
9.50372 6.78837 20.36512
6.78837 6.78837 17.64977
6.78837 9.50372 20.36512
9.50372 9.50372 17.64977
5.43070 10.86140 0.00000
5.43070 13.57675 2.71535
8.14605 13.57675 0.00000
8.14605 10.86140 2.71535
9.50372 12.21907 4.07302
6.78837 12.21907 1.35767
6.78837 14.93442 4.07302
9.50372 14.93442 1.35767
5.43070 10.86140 5.43070
5.43070 13.57675 8.14605
8.14605 13.57675 5.43070
8.14605 10.86140 8.14605
9.50372 12.21907 9.50372
6.78837 12.21907 6.78837
6.78837 14.93442 9.50372
9.50372 14.93442 6.78837
5.43070 10.86140 10.86140
5.43070 13.57675 13.57675
8.14605 13.57675 10.86140
8.14605 10.86140 13.57675
9.50372 12.21907 14.93442
6.78837 12.21907 12.21907
6.78837 14.93442 14.93442
9.50372 14.93442 12.21907
5.43070 10.86140 16.29210
5.43070 13.57675 19.00745
8.14605 13.57675 16.29210
8.14605 10.86140 19.00745
9.50372 12.21907 20.36512
6.78837 12.21907 17.64977
6.78837 14.93442 20.36512
9.50372 14.93442 17.64977
5.43070 16.29210 0.00000
5.43070 19.00745 2.71535
8.14605 19.00745 0.00000
8.14605 16.29210 2.71535
9.50372 17.64977 4.07302
6.78837 17.64977 1.35767
6.78837 20.36512 4.07302
9.50372 20.36512 1.35767
5.43070 16.29210 5.43070
5.43070 19.00745 8.14605
8.14605 19.00745 5.43070
8.14605 16.29210 8.14605
9.50372 17.64977 9.50372
6.78837 17.64977 6.78837
6.78837 20.36512 9.50372
9.50372 20.36512 6.78837
5.43070 16.29210 10.86140
5.43070 19.00745 13.57675
8.14605 19.00745 10.86140
8.14605 16.29210 13.57675
9.50372 17.64977 14.93442
6.78837 17.64977 12.21907
6.78837 20.36512 14.93442
9.50372 20.36512 12.21907
5.43070 16.29210 16.29210
5.43070 19.00745 19.00745
8.14605 19.00745 16.29210
8.14605 16.29210 19.00745
9.50372 17.64977 20.36512
6.78837 17.64977 17.64977
6.78837 20.36512 20.36512
9.50372 20.36512 17.64977
10.86140 0.00000 0.00000
10.86140 2.71535 2.71535
13.57675 2.71535 0.00000
13.57675 0.00000 2.71535
14.93442 1.35767 4.07302
12.21907 1.35767 1.35767
12.21907 4.07302 4.07302
14.93442 4.07302 1.35767
10.86140 0.00000 5.43070
10.86140 2.71535 8.14605
13.57675 2.71535 5.43070
13.57675 0.00000 8.14605
14.93442 1.35767 9.50372
12.21907 1.35767 6.78837
12.21907 4.07302 9.50372
14.93442 4.07302 6.78837
10.86140 0.00000 10.86140
10.86140 2.71535 13.57675
13.57675 2.71535 10.86140
13.57675 0.00000 13.57675
14.93442 1.35767 14.93442
12.21907 1.35767 12.21907
12.21907 4.07302 14.93442
14.93442 4.07302 12.21907
10.86140 0.00000 16.29210
10.86140 2.71535 19.00745
13.57675 2.71535 16.29210
13.57675 0.00000 19.00745
14.93442 1.35767 20.36512
12.21907 1.35767 17.64977
12.21907 4.07302 20.36512
14.93442 4.07302 17.64977
10.86140 5.43070 0.00000
10.86140 8.14605 2.71535
13.57675 8.14605 0.00000
13.57675 5.43070 2.71535
14.93442 6.78837 4.07302
12.21907 6.78837 1.35767
12.21907 9.50372 4.07302
14.93442 9.50372 1.35767
10.86140 5.43070 5.43070
10.86140 8.14605 8.14605
13.57675 8.14605 5.43070
13.57675 5.43070 8.14605
14.93442 6.78837 9.50372
12.21907 6.78837 6.78837
12.21907 9.50372 9.50372
14.93442 9.50372 6.78837
10.86140 5.43070 10.86140
10.86140 8.14605 13.57675
13.57675 8.14605 10.86140
13.57675 5.43070 13.57675
14.93442 6.78837 14.93442
12.21907 6.78837 12.21907
12.21907 9.50372 14.93442
14.93442 9.50372 12.21907
10.86140 5.43070 16.29210
10.86140 8.14605 19.00745
13.57675 8.14605 16.29210
13.57675 5.43070 19.00745
14.93442 6.78837 20.36512
12.21907 6.78837 17.64977
12.21907 9.50372 20.36512
14.93442 9.50372 17.64977
10.86140 10.86140 0.00000
10.86140 13.57675 2.71535
13.57675 13.57675 0.00000
13.57675 10.86140 2.71535
14.93442 12.21907 4.07302
12.21907 12.21907 1.35767
12.21907 14.93442 4.07302
14.93442 14.93442 1.35767
10.86140 10.86140 5.43070
10.86140 13.57675 8.14605
13.57675 13.57675 5.43070
13.57675 10.86140 8.14605
14.93442 12.21907 9.50372
12.21907 12.21907 6.78837
12.21907 14.93442 9.50372
14.93442 14.93442 6.78837
10.86140 10.86140 10.86140
10.86140 13.57675 13.57675
13.57675 13.57675 10.86140
13.57675 10.86140 13.57675
14.93442 12.21907 14.93442
12.21907 12.21907 12.21907
12.21907 14.93442 14.93442
14.93442 14.93442 12.21907
10.86140 10.86140 16.29210
10.86140 13.57675 19.00745
13.57675 13.57675 16.29210
13.57675 10.86140 19.00745
14.93442 12.21907 20.36512
12.21907 12.21907 17.64977
12.21907 14.93442 20.36512
14.93442 14.93442 17.64977
10.86140 16.29210 0.00000
10.86140 19.00745 2.71535
13.57675 19.00745 0.00000
13.57675 16.29210 2.71535
14.93442 17.64977 4.07302
12.21907 17.64977 1.35767
12.21907 20.36512 4.07302
14.93442 20.36512 1.35767
10.86140 16.29210 5.43070
10.86140 19.00745 8.14605
13.57675 19.00745 5.43070
13.57675 16.29210 8.14605
14.93442 17.64977 9.50372
12.21907 17.64977 6.78837
12.21907 20.36512 9.50372
14.93442 20.36512 6.78837
10.86140 16.29210 10.86140
10.86140 19.00745 13.57675
13.57675 19.00745 10.86140
13.57675 16.29210 13.57675
14.93442 17.64977 14.93442
12.21907 17.64977 12.21907
12.21907 20.36512 14.93442
14.93442 20.36512 12.21907
10.86140 16.29210 16.29210
10.86140 19.00745 19.00745
13.57675 19.00745 16.29210
13.57675 16.29210 19.00745
14.93442 17.64977 20.36512
12.21907 17.64977 17.64977
12.21907 20.36512 20.36512
14.93442 20.36512 17.64977
16.29210 0.00000 0.00000
16.29210 2.71535 2.71535
19.00745 2.71535 0.00000
19.00745 0.00000 2.71535
20.36512 1.35767 4.07302
17.64977 1.35767 1.35767
17.64977 4.07302 4.07302
20.36512 4.07302 1.35767
16.29210 0.00000 5.43070
16.29210 2.71535 8.14605
19.00745 2.71535 5.43070
19.00745 0.00000 8.14605
20.36512 1.35767 9.50372
17.64977 1.35767 6.78837
17.64977 4.07302 9.50372
20.36512 4.07302 6.78837
16.29210 0.00000 10.86140
16.29210 2.71535 13.57675
19.00745 2.71535 10.86140
19.00745 0.00000 13.57675
20.36512 1.35767 14.93442
17.64977 1.35767 12.21907
17.64977 4.07302 14.93442
20.36512 4.07302 12.21907
16.29210 0.00000 16.29210
16.29210 2.71535 19.00745
19.00745 2.71535 16.29210
19.00745 0.00000 19.00745
20.36512 1.35767 20.36512
17.64977 1.35767 17.64977
17.64977 4.07302 20.36512
20.36512 4.07302 17.64977
16.29210 5.43070 0.00000
16.29210 8.14605 2.71535
19.00745 8.14605 0.00000
19.00745 5.43070 2.71535
20.36512 6.78837 4.07302
17.64977 6.78837 1.35767
17.64977 9.50372 4.07302
20.36512 9.50372 1.35767
16.29210 5.43070 5.43070
16.29210 8.14605 8.14605
19.00745 8.14605 5.43070
19.00745 5.43070 8.14605
20.36512 6.78837 9.50372
17.64977 6.78837 6.78837
17.64977 9.50372 9.50372
20.36512 9.50372 6.78837
16.29210 5.43070 10.86140
16.29210 8.14605 13.57675
19.00745 8.14605 10.86140
19.00745 5.43070 13.57675
20.36512 6.78837 14.93442
17.64977 6.78837 12.21907
17.64977 9.50372 14.93442
20.36512 9.50372 12.21907
16.29210 5.43070 16.29210
16.29210 8.14605 19.00745
19.00745 8.14605 16.29210
19.00745 5.43070 19.00745
20.36512 6.78837 20.36512
17.64977 6.78837 17.64977
17.64977 9.50372 20.36512
20.36512 9.50372 17.64977
16.29210 10.86140 0.00000
16.29210 13.57675 2.71535
19.00745 13.57675 0.00000
19.00745 10.86140 2.71535
20.36512 12.21907 4.07302
17.64977 12.21907 1.35767
17.64977 14.93442 4.07302
20.36512 14.93442 1.35767
16.29210 10.86140 5.43070
16.29210 13.57675 8.14605
19.00745 13.57675 5.43070
19.00745 10.86140 8.14605
20.36512 12.21907 9.50372
17.64977 12.21907 6.78837
17.64977 14.93442 9.50372
20.36512 14.93442 6.78837
16.29210 10.86140 10.86140
16.29210 13.57675 13.57675
19.00745 13.57675 10.86140
19.00745 10.86140 13.57675
20.36512 12.21907 14.93442
17.64977 12.21907 12.21907
17.64977 14.93442 14.93442
20.36512 14.93442 12.21907
16.29210 10.86140 16.29210
16.29210 13.57675 19.00745
19.00745 13.57675 16.29210
19.00745 10.86140 19.00745
20.36512 12.21907 20.36512
17.64977 12.21907 17.64977
17.64977 14.93442 20.36512
20.36512 14.93442 17.64977
16.29210 16.29210 0.00000
16.29210 19.00745 2.71535
19.00745 19.00745 0.00000
19.00745 16.29210 2.71535
20.36512 17.64977 4.07302
17.64977 17.64977 1.35767
17.64977 20.36512 4.07302
20.36512 20.36512 1.35767
16.29210 16.29210 5.43070
16.29210 19.00745 8.14605
19.00745 19.00745 5.43070
19.00745 16.29210 8.14605
20.36512 17.64977 9.50372
17.64977 17.64977 6.78837
17.64977 20.36512 9.50372
20.36512 20.36512 6.78837
16.29210 16.29210 10.86140
16.29210 19.00745 13.57675
19.00745 19.00745 10.86140
19.00745 16.29210 13.57675
20.36512 17.64977 14.93442
17.64977 17.64977 12.21907
17.64977 20.36512 14.93442
20.36512 20.36512 12.21907
16.29210 16.29210 16.29210
16.29210 19.00745 19.00745
19.00745 19.00745 16.29210
19.00745 16.29210 19.00745
20.36512 17.64977 20.36512
17.64977 17.64977 17.64977
17.64977 20.36512 20.36512
20.36512 20.36512 17.64977

#Definition of the planewave basis set
ecut 8.0 # Maximal kinetic energy cut-off, in Hartree

#Definition of the k-point grid
kptopt 1 # Option for the automatic generation of k points, taking
# into account the symmetry
ngkpt 2 2 2 # This is a 2x2x2 grid based on the primitive vectors
nshiftk 4 # of the reciprocal space (that form a BCC lattice !),
# repeated four times, with different shifts :
shiftk 0.5 0.5 0.5
0.5 0.0 0.0
0.0 0.5 0.0
0.0 0.0 0.5
# In cartesian coordinates, this grid is simple cubic, and
# actually corresponds to the
# so-called 4x4x4 Monkhorst-Pack grid
maxnsym 20000

#Definition of the SCF procedure
nstep 100 # Maximal number of SCF cycles
toldfe 1.0d-6 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of total energy
# differ by less than toldfe (in Hartree)
# This value is way too large for most realistic studies of materials
diemac 12.0 # Although this is not mandatory, it is worth to
# precondition the SCF cycle. The model dielectric
# function used as the standard preconditioner
# is described in the "dielng" input variable section.
# Here, we follow the prescription for bulk silicon.

## After modifying the following section, one might need to regenerate the pickle database with runtests.py -r
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
#%% [files]
#%% files_to_test =
#%% tbase3_1.out, tolnlines= 0, tolabs= 0.000e+00, tolrel= 0.000e+00
#%% psp_files = 14si.pspnc
#%% [paral_info]
#%% max_nprocs = 4
#%% [extra_info]
#%% authors = Unknown
#%% keywords =
#%% description = Crystalline silicon: computation of the total energy
#%%<END TEST_INFO>

[jzwanzig]

As far as I know, Abinit doesn't have a check point facility to restart a job in the middle of an scf cycle.

You have a lot of atoms in your unit cell. How many cores are you running on? You need to be running in parallel over bands and FFT planes ( you have a small number of k points so the default parallelism isn't enough). See the variables autoparal and paral_kgb. For a system that size I would be aiming to run on several hundred cores in parallel.

[mboaks]

Professor Zwanziger,

Thank you for your reply. I already figured out the parallelization techniques. I run those in a supercomputer facility with access to hundreds of cores.

Regards,
Mawla