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标题: CP2K做QM/MM在nvt报错cpassert failed [打印本页]

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Author: liumengru 时间: 2025-3-10 16:29
标题: CP2K做QM/MM在nvt报错cpassert failed
本帖最后由 liumengru 于 2025-3-10 16:31 编辑

在进行配体蛋白质复合物使用CP2KQM/MM计算时，使用AmberTools生成了prmtop文件，并在2024.1版本cp2k进行了能量最小化，但是在进行nvt时，cp2k报错cpassert failed，我在parmed检查prmtop文件没有问题，也对PDB文件中原子名称在nvt里进行了注释，请问应该如何修改呢？(base) master@localhost:~/cp2ktest$ cp2k.popt -i nvt.inp
*******************************************************************************
*                         RESTART INFORMATION                            *
*******************************************************************************
*                                                                            *
* RESTART FILE NAME: 7M3Z_OPT-1_1000.restart                            *
*                                                                            *
* RESTARTED QUANTITIES:                                                    *
*                      CELL                                                 *
*                      COORDINATES                                        *
*                      RANDOM NUMBER GENERATOR                            *
*                      VELOCITIES                                           *
*                      PARTICLE THERMOSTAT                                  *
*                      REAL TIME PROPAGATION                               *
*                      PINT BEAD POSITIONS                                  *
*                      PINT BEAD VELOCITIES                               *
*                      PINT NOSE THERMOSTAT                               *
*                      PINT GLE THERMOSTAT                                  *
*                      HELIUM BEAD POSITIONS                               *
*                      HELIUM PERMUTATION STATE                            *
*                      HELIUM FORCES ON SOLUTE                            *
*                      HELIUM RNG STATE                                     *
*******************************************************************************

DBCSR| CPU Multiplication driver                                        XSMM (U)
DBCSR| Multrec recursion limit                                           512 (U)
DBCSR| Multiplication stack size                                        1000 (D)
DBCSR| Maximum elements for images                                  UNLIMITED (U)
DBCSR| Multiplicative factor virtual images                                  1 (U)
DBCSR| Use multiplication densification                                     T (D)
DBCSR| Multiplication size stacks                                           3 (U)
DBCSR| Use memory pool for CPU allocation                                  F (U)
DBCSR| Number of 3D layers                                              SINGLE (U)
DBCSR| Use MPI memory allocation                                           F (U)
DBCSR| Use RMA algorithm                                                    F (U)
DBCSR| Use Communication thread                                              T (U)
DBCSR| Communication thread load                                           87 (D)
DBCSR| MPI: My process id                                                    0
DBCSR| MPI: Number of processes                                              1
DBCSR| OMP: Current number of threads                                        1
DBCSR| OMP: Max number of threads                                           1
DBCSR| Split modifier for TAS multiplication algorithm                1.0E+00 (U)

  **** **** ******  **  PROGRAM STARTED AT             2025-03-10 16:30:02.875
***** ** ***  *** ** PROGRAM STARTED ON                            localhost
** **** ****** PROGRAM STARTED BY                               master
***** ** ** ** ** PROGRAM PROCESS ID                                  382
  **** **  *******  **  PROGRAM STARTED IN                /home/master/cp2ktest

CP2K| version string:                                     CP2K version 2024.1
CP2K| source code revision number:                               git:b4a17a5
CP2K| cp2kflags: omp libint fftw3 libxc libgrpp elpa parallel mpi_f08 scalapack
CP2K|          xsmm plumed2
CP2K| is freely available from                         https://www.cp2k.org/
CP2K| Program compiled at                         Tue Nov 26 20:14:02 CST 2024
CP2K| Program compiled on                                           localhost
CP2K| Program compiled for                                              local
CP2K| Data directory path                      /home/master/cp2k-2024.1/data
CP2K| Input file name                                                 nvt.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                                        system.pdb
GLOBAL| Method name                                                       CP2K
GLOBAL| Project name                                                       NVT
GLOBAL| Run type                                                          MD
GLOBAL| FFT library                                                    FFTW3
GLOBAL| Diagonalization library                                           ELPA
GLOBAL| DGEMM library                                                    BLAS
GLOBAL| Minimum number of eigenvectors for ELPA usage                      16
GLOBAL| Orthonormality check for eigenvectors                         DISABLED
GLOBAL| Matrix multiplication library                               ScaLAPACK
GLOBAL| All-to-all communication in single precision                         F
GLOBAL| FFTs using library dependent lengths                               F
GLOBAL| Grid backend                                                    AUTO
GLOBAL| Global print level                                              HIGH
GLOBAL| MPI I/O enabled                                                    T
GLOBAL| Total number of message passing processes                            1
GLOBAL| Number of threads for this process                                  1
GLOBAL| This output is from process                                        0
GLOBAL| Stack size for threads created by OpenMP (OMP_STACKSIZE)       default
GLOBAL| CPU model name                AMD Ryzen 7 6800H with Radeon Graphics
GLOBAL| CPUID                                                             1002
GLOBAL| Compiled for CPUID                                                 0

*** HINT in environment.F:920 :: The compiler target flags (generic) used ***
*** to build this binary cannot exploit all extensions of this CPU model  ***
*** (x86_avx2). Consider compiler target flags as part of FCFLAGS and    ***
*** CFLAGS (ARCH file).                                                 ***

MEMORY| system memory details [Kb]
MEMORY|                      rank 0          min          max    average
MEMORY| MemTotal             6943056    6943056    6943056    6943056
MEMORY| MemFree             5915184    5915184    5915184    5915184
MEMORY| Buffers                40684       40684       40684       40684
MEMORY| Cached                384728       384728       384728       384728
MEMORY| Slab                   94984       94984       94984       94984
MEMORY| SReclaimable          35732       35732       35732       35732
MEMORY| MemLikelyFree       6376328    6376328    6376328    6376328

*** Fundamental physical constants (SI units) ***

*** Literature: B. J. Mohr and B. N. Taylor,
***          CODATA recommended values of the fundamental physical
***          constants: 2006, Web Version 5.1
***          http://physics.nist.gov/constants

Speed of light in vacuum [m/s]                            2.99792458000000E+08
Magnetic constant or permeability of vacuum [N/A**2]    1.25663706143592E-06
Electric constant or permittivity of vacuum [F/m]       8.85418781762039E-12
Planck constant (h) [J*s]                               6.62606896000000E-34
Planck constant (h-bar) [J*s]                            1.05457162825177E-34
Elementary charge [C]                                     1.60217648700000E-19
Electron mass [kg]                                        9.10938215000000E-31
Electron g factor [ ]                                  -2.00231930436220E+00
Proton mass [kg]                                        1.67262163700000E-27
Fine-structure constant                                  7.29735253760000E-03
Rydberg constant [1/m]                                  1.09737315685270E+07
Avogadro constant [1/mol]                               6.02214179000000E+23
Boltzmann constant [J/K]                                  1.38065040000000E-23
Atomic mass unit [kg]                                     1.66053878200000E-27
Bohr radius [m]                                           5.29177208590000E-11

*** Conversion factors ***

-> [a.u.]                                           1.82288848426455E+03
[Angstrom] -> [Bohr] = [a.u.]                            1.88972613288564E+00
[a.u.] = [Bohr] -> [Angstrom]                            5.29177208590000E-01
[a.u.] ->                                           2.41888432650478E-17
[a.u.] -> [fs]                                           2.41888432650478E-02
[a.u.] -> [J]                                           4.35974393937059E-18
[a.u.] -> [N]                                           8.23872205491840E-08
[a.u.] -> [K]                                           3.15774647902944E+05
[a.u.] -> [kJ/mol]                                        2.62549961709828E+03
[a.u.] -> [kcal/mol]                                     6.27509468713739E+02
[a.u.] -> [Pa]                                           2.94210107994716E+13
[a.u.] -> [bar]                                           2.94210107994716E+08
[a.u.] -> [atm]                                           2.90362800883016E+08
[a.u.] -> [eV]                                           2.72113838565563E+01
[a.u.] -> [Hz]                                           6.57968392072181E+15
[a.u.] -> [1/cm] (wave numbers)                         2.19474631370540E+05
[a.u./Bohr**2] -> [1/cm]                                  5.14048714338585E+03

                  ************* ******** ***********
                  ************* **********************
                  ****    **** ****    ***********
                  ******** ****  *******    ****
                  *******  **** ******* ****
                  ****    ****    ****  ****
                  ****    **** **********  ****
                  ****    **** ******** ****
                  FRONTIERS IN SIMULATION TECHNOLOGY

                     C.J. Mundy, S. Balasubramanian,
                  Ken Bagchi, J. Hutter, Ari Seitsonen
                  IFW Kuo, T. Laino, J. VandeVondele
                              Version 1.0

CELL| Volume [angstrom^3]:                                     344035.962527
CELL| Vector a [angstrom]:    70.402    0.000    0.000 |a| = 70.402000
CELL| Vector b [angstrom]:    0.000 70.410    0.000 |b| = 70.410000
CELL| Vector c [angstrom]:    0.000    0.000 69.404 |c| = 69.404000
CELL| Angle (b,c), alpha [degree]:                                  90.000000
CELL| Angle (a,c), beta  [degree]:                                  90.000000
CELL| Angle (a,b), gamma [degree]:                                  90.000000
CELL| Numerically orthorhombic:                                           YES
CELL| Periodicity                                                          XYZ

CELL_REF| Volume [angstrom^3]:                                  344035.962527
CELL_REF| Vector a [angstrom 70.402    0.000    0.000 |a| = 70.402000
CELL_REF| Vector b [angstrom    0.000 70.410    0.000 |b| = 70.410000
CELL_REF| Vector c [angstrom    0.000    0.000 69.404 |c| = 69.404000
CELL_REF| Angle (b,c), alpha [degree]:                               90.000000
CELL_REF| Angle (a,c), beta  [degree]:                               90.000000
CELL_REF| Angle (a,b), gamma [degree]:                               90.000000
CELL_REF| Numerically orthorhombic:                                        YES
CELL_REF| Periodicity                                                    XYZ

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                      80       80       80
EWALD| Spline interpolation order                                           6

CELL_TOP| Volume [angstrom^3]:                                  344035.962527
CELL_TOP| Vector a [angstrom 70.402    0.000    0.000 |a| = 70.402000
CELL_TOP| Vector b [angstrom    0.000 70.410    0.000 |b| = 70.410000
CELL_TOP| Vector c [angstrom    0.000    0.000 69.404 |c| = 69.404000
CELL_TOP| Angle (b,c), alpha [degree]:                               90.000000
CELL_TOP| Angle (a,c), beta  [degree]:                               90.000000
CELL_TOP| Angle (a,b), gamma [degree]:                               90.000000
CELL_TOP| Numerically orthorhombic:                                        YES
CELL_TOP| Periodicity                                                    XYZ

*******************************************************************************
* ___                                                                      *
*  / \                                                                   *
* [ABORT]                                                                   *
*  \___/                            CPASSERT failed                         *
* |                                                                      *
*  O/|                                                                      *
* /| |                                                                      *
* / \                                                 topology_input.F:491 *
*******************************************************************************

===== Routine Calling Stack =====

         4 topology_control
         3 fist_init
         2 fist_create_force_env
         1 CP2K
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

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.
--------------------------------------------------------------------------
([size=12.573px]parmed[size=12.573px]parmed

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