NUCPRO Nuclei too close ERROR

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m775b097
Posts: 18
Joined: 26 Apr 2016, 03:55
First name(s): Matthew
Last name(s): Barclay
Affiliation: University of Kansas
Country: United States

NUCPRO Nuclei too close ERROR

Post by m775b097 » 27 Apr 2016, 16:51

Hi,

First off, I'm sorry if this is an obvious fix, but I'm new to Dalton and have been up and down this board and it didn't seem like anyone else had this problem.

I'll add the details below, but in short I keep getting an error in NUCPRO saying the nuclei are too close:
SYMGRP: Point group information
-------------------------------

@ Point group: C1
Nucleus no. 1 is too close to the 0th transformation of nucleus no. 2
DISTANCE = 0.00000D+00

X_A, X_B : 0.0000000000 0.0000000000
Y_A, Y_B : 0.0000000000 0.0000000000
Z_A, Z_B : 0.0000000000 0.0000000000

--- SEVERE ERROR, PROGRAM WILL BE ABORTED ---
Date and time (Linux) : Wed Apr 27 09:46:01 2016
Host name : n470

@ MPI MASTER, node no.: 0
@ Reason: NUCPRO: Nuclei too close.
except I've input the exact same coordinates in both visualization software (wxMacMolPlot) as well as another computing program (Gaussian09),
both confirming that the coordinates are just fine.
--is this just a bug of some sort, or am I overlooking a simple mistake?


Anyway, the full story is that I'm attempting a calculation of excited-state polarizability in DFT:

Code: Select all

**DALTON INPUT
.RUN RESPONSE
**INTEGRAL
.DIPLEN
.DEROVL
.DERHAM
**WAVE FUNCTIONS
.DFT
 B3LYP
*SCF INPUT
.THRESH
1.0D-10
**RESPONSE
*LINEAR
.DIPLEN
.FREQUE
 1
 0.0
.THCLR
1.0D-10
**END OF DALTON INPUT
(feel free, by the way, to point out any errors in the .dal file)

and, when pairing this .dal file with the following .mol geometry:

Code: Select all

BASIS
aug-cc-pVDZ
MPT polar TDDFT test
dplus1
Atomtypes=4 Angstrom Nosymmetry
Charge=6.0 Atoms=5
C       4.2079801794    -0.504128418164 -0.000552321986552
C       2.82135605544   0.0315969355655 -0.000304591208387
C       2.41775987953   1.38325199981   -0.000140598089185
C       1.04177986348   1.57874618836   1.52708305968e-05
C       0.301352992839  0.345251287216  -4.97724388992e-05
Charge=16.0 Atoms=1
S       1.44217718585   -1.05436285559  -0.000224244374914
Charge=6.0 Atoms=6
C       -1.09050903995  0.139962201481  -7.76528216736e-05
C       -2.00288388249  1.26074604903   -6.08077732803e-05
C       -3.37006292429  1.05369081901   -0.000174263058826
C       -3.9046521087   -0.253443262522 -0.000291268999888
C       -3.03477025774  -1.36348812389  -0.000278620880592
C       -1.66228923125  -1.18500489076  -0.000169329514323
Charge=1.0 Atoms=10
H       4.40380756957   -1.13779905189  -0.884595214342
H       4.40399413381   -1.13778096588  0.883200797523
H       4.93437196278   0.318447386173  -0.000474195795072
H       3.1468877854    2.19276391244   -0.000145046504337
H       0.562139756381  2.55339525472   0.000160661845955
H       -1.60780976113  2.27528609903   2.68927633066e-05
H       -4.04421878795  1.91106870551   -0.000173276033458
H       -4.98433112709  -0.403267377633 -0.000379634115914
H       -3.44683643388  -2.37320419768  -0.000354914013712
H       -1.00157535321  -2.05261078782  -0.000155789129443
I get the above error.

**The full output file is here:

Code: Select all


     ************************************************************************
     *************** Dalton - An Electronic Structure Program ***************
     ************************************************************************

    This is output from DALTON release Dalton2016.0 (2015)
         ( Web site: http://daltonprogram.org )

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

    NOTE:
     
    Dalton is an experimental code for the evaluation of molecular
    properties using (MC)SCF, DFT, CI, and CC wave functions.
    The authors accept no responsibility for the performance of
    the code or for the correctness of the results.
     
    The code (in whole or part) is provided under a licence and
    is not to be reproduced for further distribution without
    the written permission of the authors or their representatives.
     
    See the home page "http://daltonprogram.org" for further information.
     
    If results obtained with this code are published,
    the appropriate citations would be both of:
     
       K. Aidas, C. Angeli, K. L. Bak, V. Bakken, R. Bast,
       L. Boman, O. Christiansen, R. Cimiraglia, S. Coriani,
       J. Cukras, P. Dahle, E. K. Dalskov, U. Ekstroem,
       T. Enevoldsen, J. J. Eriksen, P. Ettenhuber, B. Fernandez,
       L. Ferrighi, H. Fliegl, L. Frediani, K. Hald, A. Halkier,
       C. Haettig, H. Heiberg, T. Helgaker, A. C. Hennum,
       H. Hettema, E. Hjertenaes, S. Hoest, I.-M. Hoeyvik,
       M. F. Iozzi, B. Jansik, H. J. Aa. Jensen, D. Jonsson,
       P. Joergensen, M. Kaminski, J. Kauczor, S. Kirpekar,
       T. Kjaergaard, W. Klopper, S. Knecht, R. Kobayashi, H. Koch,
       J. Kongsted, A. Krapp, K. Kristensen, A. Ligabue,
       O. B. Lutnaes, J. I. Melo, K. V. Mikkelsen, R. H. Myhre,
       C. Neiss, C. B. Nielsen, P. Norman, J. Olsen,
       J. M. H. Olsen, A. Osted, M. J. Packer, F. Pawlowski,
       T. B. Pedersen, P. F. Provasi, S. Reine, Z. Rinkevicius,
       T. A. Ruden, K. Ruud, V. Rybkin, P. Salek, C. C. M. Samson,
       A. Sanchez de Meras, T. Saue, S. P. A. Sauer,
       B. Schimmelpfennig, K. Sneskov, A. H. Steindal,
       K. O. Sylvester-Hvid, P. R. Taylor, A. M. Teale,
       E. I. Tellgren, D. P. Tew, A. J. Thorvaldsen, L. Thoegersen,
       O. Vahtras, M. A. Watson, D. J. D. Wilson, M. Ziolkowski
       and H. Agren,
       "The Dalton quantum chemistry program system",
       WIREs Comput. Mol. Sci. 2014, 4:269–284 (doi: 10.1002/wcms.1172)
     
    and
     
       Dalton, a Molecular Electronic Structure Program,
       Release Dalton2016.0 (2015), see http://daltonprogram.org
   ----------------------------------------------------------------------------

    Authors in alphabetical order (major contribution(s) in parenthesis):

  Kestutis Aidas,           Vilnius University,           Lithuania   (QM/MM)
  Celestino Angeli,         University of Ferrara,        Italy       (NEVPT2)
  Keld L. Bak,              UNI-C,                        Denmark     (AOSOPPA, non-adiabatic coupling, magnetic properties)
  Vebjoern Bakken,          University of Oslo,           Norway      (DALTON; geometry optimizer, symmetry detection)
  Radovan Bast,             UiT The Arctic U. of Norway,  Norway      (DALTON installation and execution frameworks)
  Pablo Baudin,             University of Valencia,       Spain       (Cholesky excitation energies)
  Linus Boman,              NTNU,                         Norway      (Cholesky decomposition and subsystems)
  Ove Christiansen,         Aarhus University,            Denmark     (CC module)
  Renzo Cimiraglia,         University of Ferrara,        Italy       (NEVPT2)
  Sonia Coriani,            University of Trieste,        Italy       (CC module, MCD in RESPONS)
  Janusz Cukras,            University of Trieste,        Italy       (MChD in RESPONS)
  Paal Dahle,               University of Oslo,           Norway      (Parallelization)
  Erik K. Dalskov,          UNI-C,                        Denmark     (SOPPA)
  Thomas Enevoldsen,        Univ. of Southern Denmark,    Denmark     (SOPPA)
  Janus J. Eriksen,         Aarhus University,            Denmark     (Polarizable embedding model, TDA)
  Rasmus Faber,             University of Copenhagen,     Denmark     (Vib.avg. NMR with SOPPA, parallel AO-SOPPA)
  Berta Fernandez,          U. of Santiago de Compostela, Spain       (doublet spin, ESR in RESPONS)
  Lara Ferrighi,            Aarhus University,            Denmark     (PCM Cubic response)
  Heike Fliegl,             University of Oslo,           Norway      (CCSD(R12))
  Luca Frediani,            UiT The Arctic U. of Norway,  Norway      (PCM)
  Bin Gao,                  UiT The Arctic U. of Norway,  Norway      (Gen1Int library)
  Christof Haettig,         Ruhr-University Bochum,       Germany     (CC module)
  Kasper Hald,              Aarhus University,            Denmark     (CC module)
  Asger Halkier,            Aarhus University,            Denmark     (CC module)
  Frederik Beyer Hansen,    University of Copenhagen,     Denmark     (Parallel AO-SOPPA)
  Erik D. Hedegaard,        Univ. of Southern Denmark,    Denmark     (Polarizable embedding model, QM/MM)
  Hanne Heiberg,            University of Oslo,           Norway      (geometry analysis, selected one-electron integrals)
  Trygve Helgaker,          University of Oslo,           Norway      (DALTON; ABACUS, ERI, DFT modules, London, and much more)
  Alf Christian Hennum,     University of Oslo,           Norway      (Parity violation)
  Hinne Hettema,            University of Auckland,       New Zealand (quadratic response in RESPONS; SIRIUS supersymmetry)
  Eirik Hjertenaes,         NTNU,                         Norway      (Cholesky decomposition)
  Maria Francesca Iozzi,    University of Oslo,           Norway      (RPA)
  Brano Jansik              Technical Univ. of Ostrava    Czech Rep.  (DFT cubic response)
  Hans Joergen Aa. Jensen,  Univ. of Southern Denmark,    Denmark     (DALTON; SIRIUS, RESPONS, ABACUS modules, London, and much more)
  Dan Jonsson,              UiT The Arctic U. of Norway,  Norway      (cubic response in RESPONS module)
  Poul Joergensen,          Aarhus University,            Denmark     (RESPONS, ABACUS, and CC modules)
  Maciej Kaminski,          University of Warsaw,         Poland      (CPPh in RESPONS)
  Joanna Kauczor,           Linkoeping University,        Sweden      (Complex polarization propagator (CPP) module)
  Sheela Kirpekar,          Univ. of Southern Denmark,    Denmark     (Mass-velocity & Darwin integrals)
  Wim Klopper,              KIT Karlsruhe,                Germany     (R12 code in CC, SIRIUS, and ABACUS modules)
  Stefan Knecht,            ETH Zurich,                   Switzerland (Parallel CI and MCSCF)
  Rika Kobayashi,           Australian National Univ.,    Australia   (DIIS in CC, London in MCSCF)
  Henrik Koch,              NTNU,                         Norway      (CC module, Cholesky decomposition)
  Jacob Kongsted,           Univ. of Southern Denmark,    Denmark     (Polarizable embedding model, QM/MM)
  Andrea Ligabue,           University of Modena,         Italy       (CTOCD, AOSOPPA)
  Nanna H. List             Univ. of Southern Denmark,    Denmark     (Polarizable embedding model)
  Ola B. Lutnaes,           University of Oslo,           Norway      (DFT Hessian)
  Juan I. Melo,             University of Buenos Aires,   Argentina   (LRESC, Relativistic Effects on NMR Shieldings)
  Kurt V. Mikkelsen,        University of Copenhagen,     Denmark     (MC-SCRF and QM/MM)
  Rolf H. Myhre,            NTNU,                         Norway      (Cholesky, subsystems and ECC2)
  Christian Neiss,          Univ. Erlangen-Nuernberg,     Germany     (CCSD(R12))
  Christian B. Nielsen,     University of Copenhagen,     Denmark     (QM/MM)
  Patrick Norman,           Linkoeping University,        Sweden      (Cubic response and complex frequency response in RESPONS)
  Jeppe Olsen,              Aarhus University,            Denmark     (SIRIUS CI/density modules)
  Jogvan Magnus H. Olsen,   Univ. of Southern Denmark,    Denmark     (Polarizable embedding model, QM/MM)
  Anders Osted,             Copenhagen University,        Denmark     (QM/MM)
  Martin J. Packer,         University of Sheffield,      UK          (SOPPA)
  Filip Pawlowski,          Kazimierz Wielki University,  Poland      (CC3)
  Morten N. Pedersen,       Univ. of Southern Denmark,    Denmark     (Polarizable embedding model)
  Thomas B. Pedersen,       University of Oslo,           Norway      (Cholesky decomposition)
  Patricio F. Provasi,      University of Northeastern,   Argentina   (Analysis of coupling constants in localized orbitals)
  Zilvinas Rinkevicius,     KTH Stockholm,                Sweden      (open-shell DFT, ESR)
  Elias Rudberg,            KTH Stockholm,                Sweden      (DFT grid and basis info)
  Torgeir A. Ruden,         University of Oslo,           Norway      (Numerical derivatives in ABACUS)
  Kenneth Ruud,             UiT The Arctic U. of Norway,  Norway      (DALTON; ABACUS magnetic properties and much more)
  Pawel Salek,              KTH Stockholm,                Sweden      (DALTON; DFT code)
  Claire C. M. Samson       University of Karlsruhe       Germany     (Boys localization, r12 integrals in ERI)
  Alfredo Sanchez de Meras, University of Valencia,       Spain       (CC module, Cholesky decomposition)
  Trond Saue,               Paul Sabatier University,     France      (direct Fock matrix construction)
  Stephan P. A. Sauer,      University of Copenhagen,     Denmark     (SOPPA(CCSD), SOPPA prop., AOSOPPA, vibrational g-factors)
  Bernd Schimmelpfennig,    Forschungszentrum Karlsruhe,  Germany     (AMFI module)
  Kristian Sneskov,         Aarhus University,            Denmark     (Polarizable embedding model, QM/MM)
  Arnfinn H. Steindal,      UiT The Arctic U. of Norway,  Norway      (parallel QM/MM, Polarizable embedding model)
  Casper Steinmann,         Univ. of Southern Denmark,    Denmark     (QFIT, Polarizable embedding model)
  K. O. Sylvester-Hvid,     University of Copenhagen,     Denmark     (MC-SCRF)
  Peter R. Taylor,          VLSCI/Univ. of Melbourne,     Australia   (Symmetry handling ABACUS, integral transformation)
  Andrew M. Teale,          University of Nottingham,     England     (DFT-AC, DFT-D)
  David P. Tew,             University of Bristol,        England     (CCSD(R12))
  Olav Vahtras,             KTH Stockholm,                Sweden      (triplet response, spin-orbit, ESR, TDDFT, open-shell DFT)
  David J. Wilson,          La Trobe University,          Australia   (DFT Hessian and DFT magnetizabilities)
  Hans Agren,               KTH Stockholm,                Sweden      (SIRIUS module, RESPONS, MC-SCRF solvation model)
 --------------------------------------------------------------------------------

     Date and time (Linux)  : Wed Apr 27 10:59:29 2016 
     Host name              : n470                                    

 * Work memory size             :    64000000 =  488.28 megabytes.

 * Directories for basis set searches:
   1) /mcaricato/mbarclay/daltontests/mpts1raman/outputs
   2) /panfs/pfs.acf.ku.edu/cluster/6.2/dalton/2016.0/basis


Compilation information
-----------------------

 Who compiled             | wmason
 Host                     | n113
 System                   | Linux-2.6.32-504.3.3.el6.x86_64
 CMake generator          | Unix Makefiles
 Processor                | x86_64
 64-bit integers          | OFF
 MPI                      | ON
 Fortran compiler         | /tools/cluster/6.2/openmpi/1.6.5/bin/mpif90
 Fortran compiler version | GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
 C compiler               | /tools/cluster/6.2/openmpi/1.6.5/bin/mpicc
 C compiler version       | gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
 C++ compiler             | /tools/cluster/6.2/openmpi/1.6.5/bin/mpicxx
 C++ compiler version     | unknown
 BLAS                     | /usr/lib64/atlas/libf77blas.so;/usr/lib64/atlas/li
                          | bcblas.so;/usr/lib64/atlas/libatlas.so
 LAPACK                   | /usr/lib64/atlas/libatlas.so;/usr/lib64/atlas/libl
                          | apack.so
 Static linking           | OFF
 Last Git revision        | 693735158eee69ff73df6846b9911e94803b8d7a
 Configuration time       | 2016-04-04 08:22:01.644768

 * Sequential calculation.


   Content of the .dal input file
 ----------------------------------

**DALTON INPUT                                    
.RUN RESPONSE                                     
**INTEGRAL                                        
.DIPLEN                                           
.DEROVL                                           
.DERHAM                                           
**WAVE FUNCTIONS                                  
.DFT                                              
 B3LYP                                            
*SCF INPUT                                        
.THRESH                                           
1.0D-10                                           
**RESPONSE                                        
*LINEAR                                           
.DIPLEN                                           
.FREQUE                                           
 1                                                
 0.0                                              
.THCLR                                            
1.0D-10                                           
**END OF DALTON INPUT                             


   Content of the .mol file
 ----------------------------

BASIS                                                                          
aug-cc-pVDZ                                                                    
MPT polar TDDFT test                                                           
dplus1                                                                         
Atomtypes=4 Angstrom Nosymmetry                                                
Charge=6.0 Atoms=5                                                             
C	4.2079801794	-0.504128418164	-0.000552321986552                              
C	2.82135605544	0.0315969355655	-0.000304591208387                             
C	2.41775987953	1.38325199981	-0.000140598089185                               
C	1.04177986348	1.57874618836	1.52708305968e-05                                
C	0.301352992839	0.345251287216	-4.97724388992e-05                             
Charge=16.0 Atoms=1                                                            
S	1.44217718585	-1.05436285559	-0.000224244374914                              
Charge=6.0 Atoms=6                                                             
C	-1.09050903995	0.139962201481	-7.76528216736e-05                             
C	-2.00288388249	1.26074604903	-6.08077732803e-05                              
C	-3.37006292429	1.05369081901	-0.000174263058826                              
C	-3.9046521087	-0.253443262522	-0.000291268999888                             
C	-3.03477025774	-1.36348812389	-0.000278620880592                             
C	-1.66228923125	-1.18500489076	-0.000169329514323                             
Charge=1.0 Atoms=10                                                            
H	4.40380756957	-1.13779905189	-0.884595214342                                 
H	4.40399413381	-1.13778096588	0.883200797523                                  
H	4.93437196278	0.318447386173	-0.000474195795072                              
H	3.1468877854	2.19276391244	-0.000145046504337                                
H	0.562139756381	2.55339525472	0.000160661845955                               
H	-1.60780976113	2.27528609903	2.68927633066e-05                               
H	-4.04421878795	1.91106870551	-0.000173276033458                              
H	-4.98433112709	-0.403267377633	-0.000379634115914                            
H	-3.44683643388	-2.37320419768	-0.000354914013712                             
H	-1.00157535321	-2.05261078782	-0.000155789129443                             


       *******************************************************************
       *********** Output from DALTON general input processing ***********
       *******************************************************************

 --------------------------------------------------------------------------------
   Overall default print level:    0
   Print level for DALTON.STAT:    1

    HERMIT 1- and 2-electron integral sections will be executed
    "Old" integral transformation used (limited to max 255 basis functions)
    Wave function sections will be executed (SIRIUS module)
    Dynamic molecular response properties section will be executed (RESPONSE module)
 --------------------------------------------------------------------------------


   ****************************************************************************
   *************** Output of molecule and basis set information ***************
   ****************************************************************************


    The two title cards from your ".mol" input:
    ------------------------------------------------------------------------
 1: MPT polar TDDFT test                                                    
 2: dplus1                                                                  
    ------------------------------------------------------------------------

  Coordinates are entered in Angstrom and converted to atomic units.
          - Conversion factor : 1 bohr = 0.52917721 A

  Atomic type no.    1
  --------------------
  Nuclear charge:   6.00000
  Number of symmetry independent centers:    5
  Number of basis sets to read;    2
  Basis set file used for this atomic type with Z =   6 :
     "/panfs/pfs.acf.ku.edu/cluster/6.2/dalton/2016.0/basis/aug-cc-pVDZ"

  Atomic type no.    2
  --------------------
  Nuclear charge:  16.00000
  Number of symmetry independent centers:    1
  Number of basis sets to read;    2
  Basis set file used for this atomic type with Z =  16 :
     "/panfs/pfs.acf.ku.edu/cluster/6.2/dalton/2016.0/basis/aug-cc-pVDZ"

  Atomic type no.    3
  --------------------
  Nuclear charge:   6.00000
  Number of symmetry independent centers:    6
  Number of basis sets to read;    2
  Basis set file used for this atomic type with Z =   6 :
     "/panfs/pfs.acf.ku.edu/cluster/6.2/dalton/2016.0/basis/aug-cc-pVDZ"

  Atomic type no.    4
  --------------------
  Nuclear charge:   1.00000
  Number of symmetry independent centers:   10
  Number of basis sets to read;    2
  Basis set file used for this atomic type with Z =   1 :
     "/panfs/pfs.acf.ku.edu/cluster/6.2/dalton/2016.0/basis/aug-cc-pVDZ"


                         SYMGRP: Point group information
                         -------------------------------

@    Point group: C1 
 Nucleus no.    1 is too close to the    0th transformation of nucleus no.    2
 DISTANCE =    0.00000D+00

 X_A, X_B :                  0.0000000000                  0.0000000000
 Y_A, Y_B :                  0.0000000000                  0.0000000000
 Z_A, Z_B :                  0.0000000000                  0.0000000000

  --- SEVERE ERROR, PROGRAM WILL BE ABORTED ---
     Date and time (Linux)  : Wed Apr 27 10:59:29 2016 
     Host name              : n470                                    

@ MPI MASTER, node no.:     0
@ Reason: NUCPRO: Nuclei too close.

  Total CPU  time used in DALTON:   0.01 seconds
  Total wall time used in DALTON:   0.03 seconds


 QTRACE dump of internal trace stack

 ========================
      level    module
 ========================
          6    NUCPRO      
          5    READ_MOL    
          4    READIN      
          3    HERMIT      
          2    DALTON      
          1    DALTON main 
 ========================

Please let me know what I'm doing wrong - this has been frustrating me longer than I care to admit.

Thanks,
~Matt
Last edited by m775b097 on 27 Apr 2016, 17:22, edited 1 time in total.

hjaaj
Posts: 334
Joined: 27 Jun 2013, 18:44
First name(s): Hans Jørgen
Middle name(s): Aagaard
Last name(s): Jensen
Affiliation: Universith of Southern Denmark
Country: Denmark

Re: NUCPRO Nuclei too close ERROR

Post by hjaaj » 27 Apr 2016, 17:18

Please upload the output file. (The input files are not necessary then, as the input is copied in the output.)

-- Hans Jørgen.

m775b097
Posts: 18
Joined: 26 Apr 2016, 03:55
First name(s): Matthew
Last name(s): Barclay
Affiliation: University of Kansas
Country: United States

Re: NUCPRO Nuclei too close ERROR

Post by m775b097 » 27 Apr 2016, 17:23

I'm sorry - I've edited the original message to include the output.
Thanks,
~Matt

hjaaj
Posts: 334
Joined: 27 Jun 2013, 18:44
First name(s): Hans Jørgen
Middle name(s): Aagaard
Last name(s): Jensen
Affiliation: Universith of Southern Denmark
Country: Denmark

Re: NUCPRO Nuclei too close ERROR

Post by hjaaj » 27 Apr 2016, 18:21

HI again.

Strange, it should work. And I then tried your input files, and the calculation progressed far beyond where yours stopped before I killed it.

My best guess for the cause for your problem is your compiler, gcc/gfortran version 4.4.7. Try to update to a newer gnu compiler (I am using version 5.3.0 now, but I know that versions 4.9.x also works).

m775b097
Posts: 18
Joined: 26 Apr 2016, 03:55
First name(s): Matthew
Last name(s): Barclay
Affiliation: University of Kansas
Country: United States

Re: NUCPRO Nuclei too close ERROR

Post by m775b097 » 03 May 2016, 22:32

If anyone's reading this (and comes across a similar problem), I've found the issue.

I was using a script to create .mol files and, in transcribing the geometries, I used Tab as the delimiter e.g.:
C [tab] -4.21025 [tab] -0.506234 [tab] -9.53220e-05 [linebreak]
.......which by default read as values of zero.

Long story short, spaces are required in the .mol file.

Thanks again,
~Matt

bast
Posts: 1210
Joined: 26 Aug 2013, 13:22
First name(s): Radovan
Last name(s): Bast
Affiliation: none
Country: Germany

Re: NUCPRO Nuclei too close ERROR

Post by bast » 04 May 2016, 10:36

dear Matt,
thanks for sharing the solution - good catch.
radovan

Carravetta
Posts: 6
Joined: 14 Feb 2014, 13:42
First name(s): Vincenzo
Last name(s): Carravetta
Affiliation: CNR-IPCF
Country: Italy

Re: NUCPRO Nuclei too close ERROR

Post by Carravetta » 05 May 2016, 21:57

I am afraid is not simply a problem of missing spaces. I attach an output where that error occurs because

Nucleus no. 1 is too close to the 0th transformation of nucleus no. 2

despite the option "Nosymmetry" is present in the mol file and the point group is correctly identified as C1, i.e no symmetry operation should be applied to the input geometry. Not to mention that the printed coordinates after the error message have nothing to do with the input coordinates. I tend to agree with Hans Jorgen regarding a "compiler problem" (I used "ifort" anyway) but, so far, I could not try a different one.

Vincenzo
Attachments
gs_hf_test.out
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m775b097
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Re: NUCPRO Nuclei too close ERROR

Post by m775b097 » 06 May 2016, 00:10

Hi Vincenzo,

You're probably right that it is not simply a problem of missing spaces - I am not entirely sure what, specifically, the code that reads the .mol files is looking for.
Technically, all I can say for sure is that it reads Tab as 0 somehow. And that I got it to work by using spaces.

ANYway, though I think I see your problem.
In your .mol file, your input coordinates look like:

Code: Select all

Charge=6.0 Atoms=2 Basis=Ahlrichs-VTZ                                          
C 6.0 0.00000 0.00000 0.00000                                                  
C 6.0 0.00000 0.00000 2.00000                                                  
and....again, I don't know exactly how the .mol reader works, but I am pretty sure that you don't need to repeat the 6.0 charge of C before the Cartesian coordinates.
(assuming that was what you were doing)

That part of the .mol file should look like:

Code: Select all

Charge=6.0 Atoms=2 Basis=Ahlrichs-VTZ                                          
C 0.00000 0.00000 0.00000                                                  
C 0.00000 0.00000 2.00000                                                  
Otherwise, the first value it reads (the X coordinate) is going to be 6.0, which is 6.0 Angstroms, which is 11.3383567500 Bohr,
which is exactly what it says in the .out file:

Code: Select all

 X_A, X_B :                 11.3383567500                 11.3383567500
 Y_A, Y_B :                  0.0000000000                  0.0000000000
 Z_A, Z_B :                  0.0000000000                  0.0000000000
.......and I guess after it read the two 0.00000 coordinates after that, it neglected your Z-inputs (0.00000 and 2.00000)
Thus, since it read 6.0 0.0 0.0 for both carbons, it gave the Nuclei too close error.

Hope that helped,
~Matt

kennethruud
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Re: NUCPRO Nuclei too close ERROR

Post by kennethruud » 06 May 2016, 05:06

All the information about the format of the *.mol file can be found in Chapter 26 of the Dalton manual. Please note that Dalton also reserves four places for the name of the atom, this I would recommend:

Charge=6.0 Atoms=2 Basis=Ahlrichs-VTZ
C 0.00000 0.00000 0.00000
C 0.00000 0.00000 2.00000

With the exception of the names of atoms, the rest of the input can be made free format unless I remember incorrectly (but also fixed format if you prefer), and a blank character is used to separate entries.


Best regards,

Kenneth

Carravetta
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Re: NUCPRO Nuclei too close ERROR

Post by Carravetta » 06 May 2016, 10:19

Thanks Matt, it helped of course! I got distracted by the strange error message that speaks of " 0th transformation " and I did not check my input carefully.

Vincenzo

hjaaj
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Re: NUCPRO Nuclei too close ERROR

Post by hjaaj » 07 May 2016, 08:41

Carravetta wrote:Thanks Matt, it helped of course! I got distracted by the strange error message that speaks of " 0th transformation " and I did not check my input carefully.
There is logic to it ;-) In Dalton when you use symmetry, only the symmetry-independent nuclei are stored, the remaining symmetry related nuclei are generated by performing the symmetry operations on the coordinates of the symmetry-independent nuclei. The "0th transformation" is the identity operation, i.e. the coordinates of a reference symmetry-independent nucleus.

hjaaj
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Re: NUCPRO Nuclei too close ERROR

Post by hjaaj » 07 May 2016, 08:46

m775b097 wrote:If anyone's reading this (and comes across a similar problem), I've found the issue.

I was using a script to create .mol files and, in transcribing the geometries, I used Tab as the delimiter e.g.:
C [tab] -4.21025 [tab] -0.506234 [tab] -9.53220e-05 [linebreak]
.......which by default read as values of zero.

Long story short, spaces are required in the .mol file.
Thank you for finding the reason :-) To reduce the probability of such a problem in the future I have programmed that any [tab] character in the coordinate lines of the .mol file is changed to a blank before attempting to read the coordinates. This change will be part of Dalton2016.2.

-- Hans Jørgen.

taylor
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Re: NUCPRO Nuclei too close ERROR

Post by taylor » 08 May 2016, 06:15

One should be careful manipulating tabs using Fortran. The Fortran standard does not recognize or define the character set: the requirements are something like the lower-case letters a-z are in lexical order, the upper-case letters are in lexical order, but may precede or succeed the lower-case, and the numbers 0-9 are in numerical order. There is no reference to "control characters" such as TAB, DEL, LF, etc., and as I understand it there is no lexical ordering imposed on the "special characters" like $,/,+, etc.

Now it is true that the Fortrans I'm familiar with under Linux all use the ASCII set. But if someone wants to use some completely different character set when they write their compiler/libraries/operating system, they are free to do so as I understand it, as long as they meet the requirements of the standard. Might it be safer to modify the Dalton runscript to use the tr command in Linux when the .mol file gets copied to MOLECULE.INP in the runtime directory, using tr to convert tabs to spaces on the fly? This should work in any character set (as I understand the requirements on tr).

Best regards
Pete

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