subject:"\[gmx\-users\] Problem in running CPMD with gmx\-3.3.1"

[gmx-users] Problem in running CPMD with gmx-3.3.1

2015-09-16 Thread Padmani Sandhu

Hello all,

*I am running CPMD v4.1 in hybrid with gmx-3.3.1_qmmm-1.3.2. While running
the qmmm_example ethane_em, the mdrun is evoked CPMD but the process was
stopped with an error message without completing energy minimization:*


MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 999.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--

 RESTART INFORMATION WRITTEN ON FILE  ./RESTART.1
 ***RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE  ***

 
 *  *
 *FINAL RESULTS *
 *  *
 

 
 *  ATOMIC COORDINATES  *
 
   1   H   9.953343   9.349599   8.858271
   2   H   7.204760   7.459873   8.574812
   3   H   7.204760  10.048798  10.634613
   4   H   7.204760  10.540127   7.365387
   5   C   7.885061   9.349599   8.858271
 


 


 ELECTRONIC GRADIENT:
MAX. COMPONENT =8.50745E-06 NORM =6.64506E-07

 TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 8.00
IN R-SPACE = 8.00

 (K+E1+L+N+X)   TOTAL ENERGY =   -8.04332535 A.U.
 (K)  KINETIC ENERGY =6.74712546 A.U.
 (E1=A-S+R) ELECTROSTATIC ENERGY =   -5.85407209 A.U.
 (S)   ESELF =6.64903801 A.U.
 (R) ESR =0.71345062 A.U.
 (L)LOCAL PSEUDOPOTENTIAL ENERGY =   -6.33194050 A.U.
 (N)  N-L PSEUDOPOTENTIAL ENERGY =0.56632617 A.U.
 (X) EXCHANGE-CORRELATION ENERGY =   -3.17076439 A.U.
  GRADIENT CORRECTION ENERGY =   -0.20084053 A.U.

 

*2. the local error log is showing error:*

 process id's: 0, 0, 0
 process stops in file: /home/shalu/CPMD/src/egointer_utils.mod.F90
   at line: 177
   in procedure: INTERFACE
 error message: allocation problem
 call stack:
1  cpmd


*3. I have tried to run the CPMD_inp.run file generated with the standard
./rgmx script in example with CPMD in terminal individually, it was
terminated with the same error.*

*4. In the next step I have replaced the lines*

 INTERFACE GMX
 MOLECULE CENTER OFF


with the same information from cpmd_inp.run file from CPMD-test example
files having information


  OPTIMIZE WAVEFUNCTION geometry
  molecular dynamics
  restart accumulators wavefunction coordinates velocities cell
  restart nosec nosep nosee
  restart latest
  quench bo
  ODIIS
   5
  MAXSTEP
   1000
  STORE
   5000
  TIMESTEP
   7.0
  EMASS
   500.0
  COMPRESS WRITE32





*and after it the the CPMD worked and exited successfully. *
*Can someone help me to configure the problem with gmx and CPMD interface.*







*With regards,*
*Padmani*
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Re: [gmx-users] Problem in running CPMD with gmx-3.3.1

2015-09-16 Thread Mark Abraham

Hi,

There's nothing here that points to a GROMACS-related issue. I think you
should take up the question with the CPMD community.

Mark

On Wed, Sep 16, 2015 at 1:36 PM Padmani Sandhu 
wrote:

> Hello all,
>
> *I am running CPMD v4.1 in hybrid with gmx-3.3.1_qmmm-1.3.2. While running
> the qmmm_example ethane_em, the mdrun is evoked CPMD but the process was
> stopped with an error message without completing energy minimization:*
>
>
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 999.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --
>
>  RESTART INFORMATION WRITTEN ON FILE  ./RESTART.1
>  ***RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE  ***
>
>  
>  *  *
>  *FINAL RESULTS *
>  *  *
>  
>
>  
>  *  ATOMIC COORDINATES  *
>  
>1   H   9.953343   9.349599   8.858271
>2   H   7.204760   7.459873   8.574812
>3   H   7.204760  10.048798  10.634613
>4   H   7.204760  10.540127   7.365387
>5   C   7.885061   9.349599   8.858271
>  
>
>
>  
>
>
>  ELECTRONIC GRADIENT:
> MAX. COMPONENT =8.50745E-06 NORM =6.64506E-07
>
>  TOTAL INTEGRATED ELECTRONIC DENSITY
> IN G-SPACE = 8.00
> IN R-SPACE = 8.00
>
>  (K+E1+L+N+X)   TOTAL ENERGY =   -8.04332535 A.U.
>  (K)  KINETIC ENERGY =6.74712546 A.U.
>  (E1=A-S+R) ELECTROSTATIC ENERGY =   -5.85407209 A.U.
>  (S)   ESELF =6.64903801 A.U.
>  (R) ESR =0.71345062 A.U.
>  (L)LOCAL PSEUDOPOTENTIAL ENERGY =   -6.33194050 A.U.
>  (N)  N-L PSEUDOPOTENTIAL ENERGY =0.56632617 A.U.
>  (X) EXCHANGE-CORRELATION ENERGY =   -3.17076439 A.U.
>   GRADIENT CORRECTION ENERGY =   -0.20084053 A.U.
>
>  
>
> *2. the local error log is showing error:*
>
>  process id's: 0, 0, 0
>  process stops in file: /home/shalu/CPMD/src/egointer_utils.mod.F90
>at line: 177
>in procedure: INTERFACE
>  error message: allocation problem
>  call stack:
> 1  cpmd
>
>
> *3. I have tried to run the CPMD_inp.run file generated with the standard
> ./rgmx script in example with CPMD in terminal individually, it was
> terminated with the same error.*
>
> *4. In the next step I have replaced the lines*
> 
>  INTERFACE GMX
>  MOLECULE CENTER OFF
> 
>
> with the same information from cpmd_inp.run file from CPMD-test example
> files having information
>
> 
>   OPTIMIZE WAVEFUNCTION geometry
>   molecular dynamics
>   restart accumulators wavefunction coordinates velocities cell
>   restart nosec nosep nosee
>   restart latest
>   quench bo
>   ODIIS
>5
>   MAXSTEP
>1000
>   STORE
>5000
>   TIMESTEP
>7.0
>   EMASS
>500.0
>   COMPRESS WRITE32
> 
>
>
>
>
> *and after it the the CPMD worked and exited successfully. *
> *Can someone help me to configure the problem with gmx and CPMD interface.*
>
>
>
>
>
>
>
> *With regards,*
> *Padmani*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Problem in running CPMD with gmx-3.3.1

Re: [gmx-users] Problem in running CPMD with gmx-3.3.1

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