[CP2K-user] Automated Topology Builder (ATB) force fields and CP2K
ar...@gmail.com
ar26... at gmail.com
Thu Dec 24 12:42:10 UTC 2020
Dear all,
I want to do a CP2K simulation of Chloroform using classical force fields.
The force fields are generated with Automated Topology Builder (ATB). It
gives you the force field parameters in a file called "54a7.ifp" in
Gromos96 format (which I included in the &FORCEFIELD section), the topology
file "chl_g96.top" and the structure "chl.g96" (which I included in the
&TOPOLOGY section). However the program fails with the below output (input
files are also attached). Does anyone have any idea why is the program
failing? Also, if I want to simulate N Chloroform molecules instead of only
one, do I need to explicitly write the topology of each molecule or is
there a way to say that I have N molecules of the given topology?
Best regards,
Alejandro.
DBCSR| Multiplication driver
XSMM
DBCSR| Multrec recursion
limit 512
DBCSR| Multiplication stack size
1000
DBCSR| Maximum elements for images
UNLIMITED
DBCSR| Multiplicative factor virtual
images 1
DBCSR| Multiplication size
stacks 3
DBCSR| Number of 3D layers
SINGLE
DBCSR| Use MPI memory
allocation T
DBCSR| Use RMA
algorithm F
DBCSR| Use Communication
thread T
DBCSR| Communication thread
load 0
**** **** ****** ** PROGRAM STARTED AT 2020-12-24
13:19:55.324
***** ** *** *** ** PROGRAM STARTED ON
fullerene
** **** ****** PROGRAM STARTED BY
ar612
***** ** ** ** ** PROGRAM PROCESS ID
20488
**** ** ******* ** PROGRAM STARTED IN
/cluster/data/ar612/fullerene/cp2k/eq
uilibration/mm/chl_test
CP2K| version string: CP2K
version 6.1
CP2K| source code revision number:
svn:18464
CP2K| cp2kflags: omp libint fftw3 libxc elpa=201705 elpa_qr parallel mpi3
scala
CP2K| pack xsmm libderiv_max_am1=6 libint_max_am=7 plumed2 mkl
CP2K| is freely available from
https://www.cp2k.org/
CP2K| Program compiled at Sun Mar 29 16:22:44 CEST
2020
CP2K| Program compiled on
fullerene
CP2K| Program compiled for
intel_mkl_blas_init_xsmm_xc_elpa
CP2K| Data directory path
/data/ar612/programs/intel/2017/cp2k/6.1.0/data
CP2K| Input file name
chl_test.inp
GLOBAL| Force Environment
number 1
GLOBAL| Basis set file name
BASIS_SET
GLOBAL| Potential file name
POTENTIAL
GLOBAL| MM Potential file name
MM_POTENTIAL
GLOBAL| Coordinate file name
chl.g96
GLOBAL| Method name
CP2K
GLOBAL| Project name
chl_test
GLOBAL| Preferred FFT library
FFTW3
GLOBAL| Preferred diagonalization
lib. SL
GLOBAL| Run
type MD
GLOBAL| All-to-all communication in single
precision F
GLOBAL| FFTs using library dependent
lengths F
GLOBAL| Global print
level LOW
GLOBAL| Total number of message passing
processes 1
GLOBAL| Number of threads for this
process 24
GLOBAL| This output is from
process 0
GLOBAL| CPU model name : Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max
average
MEMORY| MemTotal 49551460 49551460 49551460
49551460
MEMORY| MemFree 7285744 7285744 7285744
7285744
MEMORY| Buffers 4978552 4978552 4978552
4978552
MEMORY| Cached 34197572 34197572 34197572
34197572
MEMORY| Slab 2446576 2446576 2446576
2446576
MEMORY| SReclaimable 2401476 2401476 2401476
2401476
MEMORY| MemLikelyFree 48863344 48863344 48863344
48863344
************* ******** ***********
************* **********************
**** **** **** ***********
******** **** ******* ****
******* **** ******* ****
**** **** **** ****
**** **** ********** ****
**** **** ******** ****
FRONTIERS IN SIMULATION TECHNOLOGY
C.J. Mundy, S. Balasubramanian,
Ken Bagchi, J. Hutter, Ari Seitsonen
IFW Kuo, T. Laino, J. VandeVondele
Version 1.0
EWALD| Summation is done by:
SPME
EWALD| Alpha parameter [ ANGSTROM^-1]
0.4000
EWALD| Real Space Cutoff [ ANGSTROM]
8.4348
EWALD| G-space max. Miller index 54
54 54
EWALD| Spline interpolation
order 4
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line
Source
cp2k.ssmp 000000000A869D01 Unknown Unknown Unknown
cp2k.ssmp 000000000A867E3B Unknown Unknown Unknown
cp2k.ssmp 000000000A735374 Unknown Unknown Unknown
cp2k.ssmp 000000000A735186 Unknown Unknown Unknown
cp2k.ssmp 000000000A6C1F39 Unknown Unknown Unknown
cp2k.ssmp 000000000A6CB326 Unknown Unknown Unknown
libpthread-2.12.s 0000003C2DA0F7E0 Unknown Unknown Unknown
cp2k.ssmp 000000000116BF09 topology_gromos_m 564
topology_gromos.F
cp2k.ssmp 0000000000EEE783 topology_mp_conne 478
topology.F
cp2k.ssmp 0000000000EEDB45 topology_mp_topol 186
topology.F
cp2k.ssmp 0000000000C43747 cp_subsys_methods 158
cp_subsys_methods.F
cp2k.ssmp 0000000000C65CD8 fist_environment_ 166
fist_environment.F
cp2k.ssmp 00000000015CBAB5 fist_main_mp_fist 96
fist_main.F
cp2k.ssmp 0000000000B4B70F f77_interface_mp_ 770
f77_interface.F
cp2k.ssmp 0000000000496F1C cp2k_runs_mp_run_ 271
cp2k_runs.F
cp2k.ssmp 0000000000482813 MAIN__ 281 cp2k.F
cp2k.ssmp 000000000048149E Unknown Unknown Unknown
libc-2.12.so 0000003C2D61ED1D __libc_start_main Unknown Unknown
cp2k.ssmp 0000000000481329 Unknown Unknown Unknown
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