ESP charges of a cluster

Sahan92

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Jul 9, 2020, 12:28:30 AM7/9/20

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Hi all,

First thank you for approving my request to join the group. I am trying to find the ESP charges of a small Nb cluster. But the output always shows the following message. Hope someone can answer this question.

attached are the pictures for my input file and the errors I'm seeing with the output file. Sorry for not being able to put everything in a single picture.

Thank you,

Sahan

input.png

error1.png

error2.png

error3.png

error4.png

error5.png

Edoardo Aprà

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Jul 9, 2020, 12:48:17 AM7/9/20

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Sahan,

Please post text files. Images are not the best format.

I would suggest the following changes:

1. add the line

start mns

at the beginning of the file.

2. add the line

vectors output msn.movecs

in the dft section.

Sahan92

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Jul 9, 2020, 3:47:42 AM7/9/20

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Edoardo,

Im sorry about the picture format. So I made the changes to the input file but the error still persists.

Input file

start mns

title mns_charges

echo

print medium

geometry noautosym noautoz

O 0.978388 -0.649188 -4.146523

Si 0.015398 -2.043513 -4.029607

O -0.422971 -2.543995 -5.517392

Nb 2.568409 0.349046 -2.856745

O 1.945492 1.640782 -3.821197

O 1.992417 0.801159 -1.076727

O 4.434042 0.426765 -3.347543

H -0.960863 -3.323558 -5.443552

end

basis

Nb library lanl2dz_ecp

O library cc-pvdz

Si library cc-pvdz

H library cc-pvdz

end

ecp

Nb library lanl2dz_ecp

end

dft

vectors output mns.movecs

iterations 5000

xc b3lyp

decomp

end

driver

maxiter 500

end

task esp

Output error - final few lines

**********

2:2: * 2: esp: movecs_read_header failed 2 *:: 2

(rank:2 hostname:r07r22n04 pid:6350):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

3:3: * 3: esp: movecs_read_header failed 3 *:: 3

(rank:3 hostname:r07r22n04 pid:6351):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

4:4: * 4: esp: movecs_read_header failed 4 *:: 4

(rank:4 hostname:r07r22n04 pid:6352):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

5:5: * 5: esp: movecs_read_header failed 5 *:: 5

(rank:5 hostname:r07r22n04 pid:6353):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

6:6: * 6: esp: movecs_read_header failed 6 *:: 6

(rank:6 hostname:r07r22n04 pid:6354):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

7:7: * 7: esp: movecs_read_header failed 7 *:: 7

(rank:7 hostname:r07r22n04 pid:6355):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

* 0: esp: movecs_read_header failed 0

**********

0:0::: -1

1:1: * 1: esp: movecs_read_header failed 1 *:: 1

(rank:0 hostname:r07r22n04 pid:6348):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

(rank:1 hostname:r07r22n04 pid:6349):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

===================================================================================

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

= RANK 0 PID 6348 RUNNING AT r07r22n04

= EXIT STATUS: 5

this doesn't seem to take me anywhere. can you please help me with this.

Edoardo Aprà

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Jul 9, 2020, 3:51:49 AM7/9/20

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Please post the complete output file

On Wednesday, July 8, 2020 at 9:28:30 PM UTC-7, Sahan92 wrote:

Sahan Godahewa

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Jul 9, 2020, 12:33:57 PM7/9/20

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Hi, this is the complete output file. I’m running this on a cluster btw.

Sahan.

Job information

---------------

hostname = r07r22n04

program = nwchem

date = Thu Jul 9 00:28:44 2020

compiled = Thu_Jun_20_14:43:36_2019

source = /tmp/build/nwchem-6.8.1

nwchem branch = 6.8.1

nwchem revision = v6.8-133-ge032219

ga revision = 5.6.5

use scalapack = F

input = mns.nw

prefix = mns.

data base = ./mns.db

status = startup

nproc = 8

time left = -1s

Memory information

------------------

heap = 13107198 doubles = 100.0 Mbytes

stack = 13107195 doubles = 100.0 Mbytes

global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)

total = 52428793 doubles = 400.0 Mbytes

verify = yes

hardfail = no

Directory information

---------------------

0 permanent = .

0 scratch = .

NWChem Input Module

-------------------

mns_charges

-----------

Scaling coordinates for geometry "geometry" by 1.889725989

(inverse scale = 0.529177249)

Geometry "geometry" -> ""

-------------------------

Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)

No. Tag Charge X Y Z

---- ---------------- ---------- -------------- -------------- --------------

1 O 8.0000 -0.85472056 -0.43858727 -0.78965164

2 Si 14.0000 -1.81771056 -1.83291227 -0.67273564

3 O 8.0000 -2.25607956 -2.33339427 -2.16052064

4 Nb 41.0000 0.73530044 0.55964673 0.50012636

5 O 8.0000 0.11238344 1.85138273 -0.46432564

6 O 8.0000 0.15930844 1.01175973 2.28014436

7 O 8.0000 2.60093344 0.63736573 0.00932836

8 H 1.0000 -2.79397156 -3.11295727 -2.08668064

Atomic Mass

-----------

O 15.994910

Si 27.976930

Nb 92.906000

H 1.007825

Effective nuclear repulsion energy (a.u.) 695.5011970826

Nuclear Dipole moment (a.u.)

----------------------------

X Y Z

---------------- ---------------- ----------------

-0.0000000000 -0.0000000000 -0.0000000000

XYZ format geometry

-------------------

8

Geometry

O -0.85472056 -0.43858727 -0.78965164

Si -1.81771056 -1.83291227 -0.67273564

O -2.25607956 -2.33339427 -2.16052064

Nb 0.73530044 0.55964673 0.50012636

O 0.11238344 1.85138273 -0.46432564

O 0.15930844 1.01175973 2.28014436

O 2.60093344 0.63736573 0.00932836

H -2.79397156 -3.11295727 -2.08668064

==============================================================================

internuclear distances

------------------------------------------------------------------------------

center one | center two | atomic units | angstroms

------------------------------------------------------------------------------

2 Si | 1 O | 3.20984 | 1.69858

3 O | 2 Si | 3.07982 | 1.62977

4 Nb | 1 O | 4.30433 | 2.27775

5 O | 4 Nb | 3.26588 | 1.72823

6 O | 4 Nb | 3.63724 | 1.92474

7 O | 4 Nb | 3.64845 | 1.93068

8 H | 3 O | 1.79524 | 0.95000

------------------------------------------------------------------------------

number of included internuclear distances: 7

==============================================================================

internuclear angles

------------------------------------------------------------------------------

center 1 | center 2 | center 3 | degrees

------------------------------------------------------------------------------

2 Si | 1 O | 4 Nb | 135.77

1 O | 2 Si | 3 O | 109.98

2 Si | 3 O | 8 H | 109.47

1 O | 4 Nb | 5 O | 76.11

1 O | 4 Nb | 6 O | 114.69

:

1 O | 4 Nb | 7 O | 123.25

5 O | 4 Nb | 6 O | 103.45

5 O | 4 Nb | 7 O | 100.16

6 O | 4 Nb | 7 O | 120.99

------------------------------------------------------------------------------

number of included internuclear angles: 9

==============================================================================

warning:::::::::::::: from_environment

NWCHEM_BASIS_LIBRARY set to: <

/panfs/pfs.local/software/7/install/nwchem/6.8.1/data/libraries>

but file does not exist !

using .nwchemrc or compiled library

library name resolved from: .nwchemrc

library file name is: <

/panfs/pfs.local/software/7/install/nwchem/6.8.1/data/libraries/>

**** WARNING Zero Coefficient **** on atom " Nb"

:

angular momentum value: 0 standard basis set name: "lanl2dz ecp"

input line that generated warning:

721: 0.1454000 0.0000000 0.9969155

Basis "ao basis" -> "" (cartesian)

-----

Nb (Niobium)

------------

Exponent Coefficients

-------------- ---------------------------------------------------------

1 S 2.18200000E+00 -0.884614

1 S 1.20900000E+00 1.103377

1 S 4.16500000E-01 0.629878

2 S 2.18200000E+00 0.779029

2 S 1.20900000E+00 -1.075279

2 S 4.16500000E-01 -1.150601

2 S 1.45400000E-01 0.996915

3 S 3.92000000E-02 1.000000

4 P 4.51900000E+00 -0.081730

4 P 9.40600000E-01 0.699511

4 P 3.49200000E-01 0.398100

5 P 4.10600000E-01 -0.121218

5 P 7.52000000E-02 1.048048

6 P 2.47000000E-02 1.000000

7 D 3.46600000E+00 0.031598

7 D 9.93800000E-01 0.483431

7 D 3.35000000E-01 0.616489

8 D 1.02400000E-01 1.000000

O (Oxygen)

----------

Exponent Coefficients

1 S 1.17200000E+04 0.000710

1 S 1.75900000E+03 0.005470

1 S 4.00800000E+02 0.027837

1 S 1.13700000E+02 0.104800

1 S 3.70300000E+01 0.283062

1 S 1.32700000E+01 0.448719

1 S 5.02500000E+00 0.270952

1 S 1.01300000E+00 0.015458

2 S 1.17200000E+04 -0.000160

2 S 1.75900000E+03 -0.001263

2 S 4.00800000E+02 -0.006267

2 S 1.13700000E+02 -0.025716

2 S 3.70300000E+01 -0.070924

2 S 1.32700000E+01 -0.165411

2 S 5.02500000E+00 -0.116955

2 S 1.01300000E+00 0.557368

3 S 3.02300000E-01 1.000000

4 P 1.77000000E+01 0.043018

4 P 3.85400000E+00 0.228913

4 P 1.04600000E+00 0.508728

5 P 2.75300000E-01 1.000000

6 D 1.18500000E+00 1.000000

Si (Silicon)

------------

Exponent Coefficients

-------------- ---------------------------------------------------------

1 S 7.88600000E+04 0.000270

1 S 1.18200000E+04 0.002097

1 S 2.69200000E+03 0.010851

1 S 7.63400000E+02 0.043675

1 S 2.49600000E+02 0.137653

1 S 9.02800000E+01 0.316644

1 S 3.52900000E+01 0.418581

1 S 1.45100000E+01 0.210212

1 S 4.05300000E+00 0.014495

1 S 1.48200000E+00 -0.002036

1 S 2.51700000E-01 0.000624

2 S 7.88600000E+04 -0.000072

2 S 1.18200000E+04 -0.000555

2 S 2.69200000E+03 -0.002938

2 S 7.63400000E+02 -0.011769

2 S 2.49600000E+02 -0.040291

2 S 9.02800000E+01 -0.100609

2 S 3.52900000E+01 -0.196528

2 S 1.45100000E+01 -0.102382

2 S 4.05300000E+00 0.527190

2 S 1.48200000E+00 0.593251

2 S 2.51700000E-01 0.033265

3 S 7.88600000E+04 0.000019

3 S 1.18200000E+04 0.000142

3 S 2.69200000E+03 0.000752

3 S 7.63400000E+02 0.003023

3 S 2.49600000E+02 0.010368

3 S 9.02800000E+01 0.026256

3 S 3.52900000E+01 0.052399

3 S 1.45100000E+01 0.029096

3 S 4.05300000E+00 -0.178003

3 S 1.48200000E+00 -0.346874

3 S 2.51700000E-01 0.623020

4 S 9.24300000E-02 1.000000

5 P 3.15900000E+02 0.003927

5 P 7.44200000E+01 0.029881

5 P 2.34800000E+01 0.127212

5 P 8.48800000E+00 0.320943

5 P 3.21700000E+00 0.455429

5 P 1.22900000E+00 0.268563

5 P 2.96400000E-01 0.018834

6 P 3.15900000E+02 -0.000858

6 P 7.44200000E+01 -0.006303

6 P 2.34800000E+01 -0.028826

6 P 8.48800000E+00 -0.069456

6 P 3.21700000E+00 -0.119493

6 P 1.22900000E+00 -0.019958

6 P 2.96400000E-01 0.510268

7 P 8.76800000E-02 1.000000

8 D 2.75000000E-01 1.000000

H (Hydrogen)

------------

Exponent Coefficients

-------------- ---------------------------------------------------------

1 S 1.30100000E+01 0.019685

1 S 1.96200000E+00 0.137977

1 S 4.44600000E-01 0.478148

2 S 1.22000000E-01 1.000000

3 P 7.27000000E-01 1.000000

Summary of "ao basis" -> "" (cartesian)

------------------------------------------------------------------------------

Tag Description Shells Functions and Types

---------------- ------------------------------ ------ ---------------------

Nb lanl2dz ecp 8 24 3s3p2d

O cc-pvdz 6 15 3s2p1d

Si cc-pvdz 8 19 4s3p1d

H cc-pvdz 3 5 2s1p

warning:::::::::::::: from_environment

NWCHEM_BASIS_LIBRARY set to: <

/panfs/pfs.local/software/7/install/nwchem/6.8.1/data/libraries>

but file does not exist !

using .nwchemrc or compiled library

library name resolved from: .nwchemrc

library file name is: <

/panfs/pfs.local/software/7/install/nwchem/6.8.1/data/libraries/>

ECP "ecp basis" -> "" (cartesian)

-----

Nb (Niobium) Replaces 28 electrons

-------------------------------------

Channel R-exponent Exponent Coefficients

------------ ---------------------------------------------------------

1 U L Both 0.00 342.963841 -0.044740

1 U L Both 1.00 139.930801 -20.053510

1 U L Both 2.00 43.352340 -103.724402

1 U L Both 2.00 12.444853 -41.045916

1 U L Both 2.00 4.320484 -4.204622

2 U-s Both 0.00 112.863062 2.796467

2 U-s Both 1.00 22.967868 42.884579

2 U-s Both 2.00 4.934067 75.187697

3 U-p Both 0.00 63.680196 4.946185

3 U-p Both 1.00 23.091243 24.831638

3 U-p Both 2.00 24.428365 137.918329

3 U-p Both 2.00 4.231009 50.977847

4 U-d Both 0.00 99.335964 3.006406

4 U-d Both 1.00 64.058647 25.534746

4 U-d Both 2.00 37.089101 178.959745

4 U-d Both 2.00 12.070857 92.957749

4 U-d Both 2.00 3.157532 18.474426

NWChem Electrostatic Potential Fit Module

-----------------------------------------

Atom parameters

Number of atoms is 8

Number of basis functions is 123

Grid parameters

Maximum number of grid points is 2667

Number of grid points is 2666

Grid range 0.300000 nm

Grid spacing 0.050000 nm

Probe radius 0.070000 nm

Atom radius factor 1.000000

Atomic radii

1 0.100000

8 0.136000

13 0.195000

14 0.187000

FASTESP F

using M.O. file = ./mns.movecs

movecs_read_header: failed to open ./mns.movecs IERR = 29

**********

2:2: * 2: esp: movecs_read_header failed 2 *:: 2

(rank:2 hostname:r07r22n04 pid:6350):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

3:3: * 3: esp: movecs_read_header failed 3 *:: 3

(rank:3 hostname:r07r22n04 pid:6351):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

4:4: * 4: esp: movecs_read_header failed 4 *:: 4

(rank:4 hostname:r07r22n04 pid:6352):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

5:5: * 5: esp: movecs_read_header failed 5 *:: 5

(rank:5 hostname:r07r22n04 pid:6353):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

6:6: * 6: esp: movecs_read_header failed 6 *:: 6

(rank:6 hostname:r07r22n04 pid:6354):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

7:7: * 7: esp: movecs_read_header failed 7 *:: 7

(rank:7 hostname:r07r22n04 pid:6355):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

* 0: esp: movecs_read_header failed 0

**********

0:0::: -1

1:1: * 1: esp: movecs_read_header failed 1 *:: 1

(rank:0 hostname:r07r22n04 pid:6348):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

(rank:1 hostname:r07r22n04 pid:6349):ARMCI DASSERT fail. ../../ga-5.6.5/armci/src/common/armci.c:ARMCI_Error():208 cond:0

===================================================================================

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

= RANK 0 PID 6348 RUNNING AT r07r22n04

= EXIT STATUS: 5

===================================================================================

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

= RANK 1 PID 6349 RUNNING AT r07r22n04

= KILLED BY SIGNAL: 9 (Killed)

===================================================================================

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

= RANK 2 PID 6350 RUNNING AT r07r22n04

= EXIT STATUS: 5

===================================================================================

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

= RANK 3 PID 6351 RUNNING AT r07r22n04

= KILLED BY SIGNAL: 9 (Killed)

===================================================================================

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Edoardo Aprà

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Jul 9, 2020, 2:05:07 PM7/9/20

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I think that your problem is that you are missing the line

task dft energy

before the line

task esp

The calculation needs to generate the molecular orbitals (mns.movecs) before running the ESP task

Sahan Godahewa

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Jul 9, 2020, 4:02:51 PM7/9/20

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Thank you so much, worked like a charm!

To view this discussion on the web visit https://groups.google.com/d/msgid/nwchem-forum/037042c4-9a8e-4aa0-b453-2f78c1f61045n%40googlegroups.com.

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