I am having problem with running the benzene example that comes with the nwchem6.6, below is the output of the run:
Job information
---------------
hostname = node38
program = /home/projects/HPCMON/apps/nwchem-6.6/bin/LINUX64/nwchem
date = Fri Nov 3 21:05:12 2017
compiled = Sun_Oct_29_19:58:24_2017
source = /home/projects/HPCMON/apps/nwchem-6.6
nwchem branch = 6.6
nwchem revision = 27746
ga revision = 10594
input = benzene.nw
prefix = benzene.
data base = ./benzene.db
status = startup
nproc = 16
time left = -1s
Memory information
------------------
heap = 13107200 doubles = 100.0 Mbytes
stack = 13107197 doubles = 100.0 Mbytes
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
total = 52428797 doubles = 400.0 Mbytes
verify = yes
hardfail = no
Directory information
---------------------
0 permanent = .
0 scratch = .
NWChem Input Module
-------------------
Prepare Module
--------------
Force field
Directories used for fragment and segment files
Parameter files used to resolve force field parameters
PDB geometry benzene.pdb
Creating fragment for residue bnz
Fragment bnz
num name type link cntr grp pgrp charge polarizab
1 C1 0 6 0 1 1 0.000000 0.000000
2 H1 0 0 0 1 1 0.000000 0.000000
3 C2 0 6 0 1 1 0.000000 0.000000
4 H2 0 0 0 1 1 0.000000 0.000000
5 C3 0 6 0 1 1 0.000000 0.000000
6 H3 0 0 0 1 1 0.000000 0.000000
7 C4 0 6 0 1 1 0.000000 0.000000
8 H4 0 0 0 1 1 0.000000 0.000000
9 C5 0 6 0 1 1 0.000000 0.000000
10 H5 0 0 0 1 1 0.000000 0.000000
11 C6 0 6 0 1 1 0.000000 0.000000
12 H6 0 0 0 1 1 0.000000 0.000000
------------
total charge 0.000000
Connectivity
1- 2
1- 3
1- 11
3- 4
3- 5
5- 6
5- 7
7- 8
7- 9
9- 10
9- 11
11- 12
Created fragment bnz.frg_TMP
Unresolved atom types in fragment bnz
**********
* 0: pre_mkfrg failed 9999
**********
0::Received an Error in Communication
The bnz.frg_TMP:
- This is an automatically generated fragment file
- Atom types and connectivity were derived from coordinates
- Atomic partial charges are crude estimates
- 11/03/17 21:05:12
$bnz
12 1 1 0
bnz
1 C1 0 6 0 1 1 0.000000 0.000000
2 H1 0 0 0 1 1 0.000000 0.000000
3 C2 0 6 0 1 1 0.000000 0.000000
4 H2 0 0 0 1 1 0.000000 0.000000
5 C3 0 6 0 1 1 0.000000 0.000000
6 H3 0 0 0 1 1 0.000000 0.000000
7 C4 0 6 0 1 1 0.000000 0.000000
8 H4 0 0 0 1 1 0.000000 0.000000
9 C5 0 6 0 1 1 0.000000 0.000000
10 H5 0 0 0 1 1 0.000000 0.000000
11 C6 0 6 0 1 1 0.000000 0.000000
12 H6 0 0 0 1 1 0.000000 0.000000
1 2
1 3
1 11
3 4
3 5
5 6
5 7
7 8
7 9
9 10
9 11
11 12
The bnz.frg file:
- This is an automatically generated fragment file
- Atom types and connectivity were derived from coordinates
- Atomic partial charges are crude estimates
- 12/08/04 15:18:43
$bnz
12 1 1 0
bnz
1 C1 CA 0 1 0 1 1 -0.050000 0.000000
2 H1 HA 0 0 0 1 1 0.050000 0.000000
3 C2 CA 0 1 0 1 1 -0.050000 0.000000
4 H2 HA 0 0 0 1 1 0.050000 0.000000
5 C3 CA 0 1 0 1 1 -0.050000 0.000000
6 H3 HA 0 0 0 1 1 0.050000 0.000000
7 C4 CA 0 1 0 1 1 -0.050000 0.000000
8 H4 HA 0 0 0 1 1 0.050000 0.000000
9 C5 CA 0 1 0 1 1 -0.050000 0.000000
10 H5 HA 0 0 0 1 1 0.050000 0.000000
11 C6 CA 0 1 0 1 1 -0.050000 0.000000
12 H6 HA 0 0 0 1 1 0.050000 0.000000
1 2
1 3
1 11
3 4
3 5
5 6
5 7
7 8
7 9
9 10
9 11
11 12
Any idea?
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