Hello everyone,
I meet a problem about the “python command”. when I define a python function and invoke it to evaluate the “TEMPCORE variable” as the “ctempcore function” in the following script shows, the error about segmentation fault reports and kills the process. The python is successfully embeded in lammps and the “loop function” can work well.
Can anybody give some suggestions on how to solve the problem?
Thanks a lot!
Here are the input scripts:
variables input
variable DT equal 4.0 #time step
variable T equal 0.25e6
variable A equal 200
variable r equal 10 #radius of indent
variable R equal 30 #radius of sphere region
variable L equal 35 #half length of system scale
variable DELTA equal 20 #redefine fix npt after DELTA timesteps
variable THERMO equal 250 #print thermo after THERMO timesteps
variable RESTART equal 62500 #write restart after RESTART timesteps
variable Pstart equal 1000.0-10.0*$A/$Tstepdt
variable Pstop equal 1000.0-10.0*$A/T*(step+{DELTA})*dt
init
units real
dimension 3
boundary p p p
atom_style full
timestep ${DT}
create geometry
pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
bond_style harmonic
angle_style harmonic
special_bonds charmm
read_data data.droplet_npt
regions & groups
region core sphere $L $L $L $R units box side in
group core dynamic all region core every 1
computes
compute tcore core temp
variables output
variable N equal count(all,core)
variable TEMPCORE python ctempcore
functions
python ctempcore input 2 SELF v_N return v_TEMPCORE format pif here “”"
def ctempcore(lmpptr,N):
from lammps import lammps
lmp=lammps(ptr=lmpptr)
if N>1000:
return lmp.extract_compute(tcore,0,0)
else:
return 298
“”"
python loop input 5 SELF v_NT v_T v_DT v_DELTA format pfffi here “”"
def loop(lmpptr,NT,T,DT,DELTA):
from lammps import lammps
lmp = lammps(ptr=lmpptr)
for i in range(0,int(NTT/DT/DELTA)):
lmp.command("fix barostat all npt temp 298.0 298.0 (100.0*dt) iso {Pstart} {Pstop} (250.0dt) drag 1.0")
lmp.command(“run ${DELTA} pre yes post yes”)
lmp.command(“unfix barostat”)
“”"
fixes
fix 0 all indent 10.0 sphere $L $L $L r units box
fix 1 all shake 0.0001 20 0 b 1 a 1
fix print_tempcore all print 1 "{TEMPCORE}" file tempcore.dat screen no title “”
fix print_n all print 1 “${N}” file n.dat screen no title “”
run
thermo_style custom step temp press
thermo {THERMO}
restart {RESTART} restart.droplet
python loop invoke
Here are the error messages:
[ubuntu:04018] *** Process received signal ***
[ubuntu:04018] Signal: Segmentation fault (11)
[ubuntu:04018] Signal code: Address not mapped (1)
[ubuntu:04018] Failing at address: 0x18
[ubuntu:04018] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10330)[0x7f776ca06330]
[ubuntu:04018] [ 1] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(PyObject_Call+0x2a)[0x7f776c5a808a]
[ubuntu:04018] [ 2] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47)[0x7f776c63b5f7]
[ubuntu:04018] [ 3] ./lmp_mpi(_ZN9LAMMPS_NS6Python15invoke_functionEiPc+0x1fd)[0x8ac5bd]
[ubuntu:04018] [ 4] ./lmp_mpi(_ZN9LAMMPS_NS8Variable8retrieveEPc+0x523)[0x8feca3]
[ubuntu:04018] [ 5] ./lmp_mpi(_ZN9LAMMPS_NS5Input10substituteERPcS2_RiS3_i+0x3ad)[0x69c6dd]
[ubuntu:04018] [ 6] ./lmp_mpi(_ZN9LAMMPS_NS8FixPrint11end_of_stepEv+0x4e)[0x610e9e]
[ubuntu:04018] [ 7] ./lmp_mpi(_ZN9LAMMPS_NS6Modify11end_of_stepEv+0x78)[0x6c83b8]
[ubuntu:04018] [ 8] ./lmp_mpi(_ZN9LAMMPS_NS6Verlet3runEi+0x49e)[0x90a71e]
[ubuntu:04018] [ 9] ./lmp_mpi(_ZN9LAMMPS_NS3Run7commandEiPPc+0x8ec)[0x8d8cec]
[ubuntu:04018] [10] ./lmp_mpi(_ZN9LAMMPS_NS5Input15command_creatorINS_3RunEEEvPNS_6LAMMPSEiPPc+0x26)[0x6a6216]
[ubuntu:04018] [11] ./lmp_mpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0x7e1)[0x6a46b1]
[ubuntu:04018] [12] ./lmp_mpi(ZN9LAMMPS_NS5Input3oneEPKc+0x85)[0x6a5445]
[ubuntu:04018] [13] /usr/lib/x86_64-linux-gnu/libffi.so.6(ffi_call_unix64+0x4c)[0x7f77601d6adc]
[ubuntu:04018] [14] /usr/lib/x86_64-linux-gnu/libffi.so.6(ffi_call+0x1fc)[0x7f77601d640c]
[ubuntu:04018] [15] /usr/lib/python2.7/lib-dynload/ctypes.x86_64-linux-gnu.so(ctypes_callproc+0x48e)[0x7f77606ce5fe]
[ubuntu:04018] [16] /usr/lib/python2.7/lib-dynload/ctypes.x86_64-linux-gnu.so(+0x15f9e)[0x7f77606cff9e]
[ubuntu:04018] [17] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f776c5a80a3]
[ubuntu:04018] [18] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x2316)[0x7f776c5cf2d6]
[ubuntu:04018] [19] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x80d)[0x7f776c5d3c3d]
[ubuntu:04018] [20] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x48d8)[0x7f776c5d1898]
[ubuntu:04018] [21] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x80d)[0x7f776c5d3c3d]
[ubuntu:04018] [22] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(+0x141dd0)[0x7f776c5d3dd0]
[ubuntu:04018] [23] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f776c5a80a3]
[ubuntu:04018] [24] /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47)[0x7f776c63b5f7]
[ubuntu:04018] [25] ./lmp_mpi(_ZN9LAMMPS_NS6Python15invoke_functionEiPc+0x1fd)[0x8ac5bd]
[ubuntu:04018] [26] ./lmp_mpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0x9bc)[0x6a488c]
[ubuntu:04018] [27] ./lmp_mpi(_ZN9LAMMPS_NS5Input4fileEv+0x312)[0x6a5192]
[ubuntu:04018] [28] ./lmp_mpi(main+0x46)[0x4a2226]
[ubuntu:04018] [29] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f776b5ecf45]
[ubuntu:04018] *** End of error message ***
Segmentation fault (core dumped)