Dear Michael,
Your assumption is right, I had made changes in the files from 3.3.0 version; but when I am trying to install master on my system I get the following error while executing 'make' (after running bootstrap, and configure).:~/espresso-master$ make
Making all in config
make[1]: Entering directory `/home/harmanjit/espresso-master/config'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/harmanjit/espresso-master/config'
Making all in src
make[1]: Entering directory `/home/harmanjit/espresso-master/src'
make all-recursive
make[2]: Entering directory `/home/harmanjit/espresso-master/src'
Making all in core
make[3]: Entering directory `/home/harmanjit/espresso-master/src/core'
GEN myconfig-final.hpp <= ./myconfig-default.hpp
make all-am
make[4]: Entering directory `/home/harmanjit/espresso-master/src/core'
GEN myconfig-final.hpp <= ./myconfig-default.hpp
GEN config-version.cpp
make[4]: Leaving directory `/home/harmanjit/espresso-master/src/core'
make[3]: Leaving directory `/home/harmanjit/espresso-master/src/core'
Making all in tcl
make[3]: Entering directory `/home/harmanjit/espresso-master/src/tcl'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/harmanjit/espresso-master/src/tcl'
Making all in python/espressomd
make[3]: Entering directory `/home/harmanjit/espresso-master/src/python/espressomd'
make all-am
make[4]: Entering directory `/home/harmanjit/espresso-master/src/python/espressomd'
GEN python-all
GEN _init.so
CXXLD _system.la
GEN _system.so
CXXLD particle_data.la
GEN particle_data.so
CXXLD analyze.la
GEN analyze.so
CXXLD cellsystem.la
GEN cellsystem.so
GEN changeVolume.so
GEN code_info.so
GEN cuda_init.so
GEN debye_hueckel.so
GEN integrate.so
CYTHON interactions.cpp
Error compiling Cython file:
------------------------------------------------------------
...
cdef extern from "interaction_data.hpp":
cdef enum OverlappedBondedInteraction: OVERLAP_UNKNOWN = 0, OVERLAP_BOND_LENGTH, OVERLAP_BOND_ANGLE,\
OVERLAP_BOND_DIHEDRAL
cdef extern from "overlap.hpp":
int overlapped_bonded_set_params(int bond_type, OverlappedBondedInteraction overlap_type,\
char * filename);
^
------------------------------------------------------------
interactions.pxd:284:22: Syntax error in C variable declaration
Error compiling Cython file:
------------------------------------------------------------
...
if self._params["cutoff"]<0:
raise ValueError("Lennard-Jones cutoff has to be >=0")
return True
def _getParamsFromEsCore(self):
cdef IA_parameters* iaParams
^
------------------------------------------------------------
interactions.pyx:154:13: 'IA_parameters' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
raise ValueError("Lennard-Jones cutoff has to be >=0")
return True
def _getParamsFromEsCore(self):
cdef IA_parameters* iaParams
iaParams = get_ia_param(self._partTypes[0],self._partTypes[1])
^
------------------------------------------------------------
interactions.pyx:155:32: undeclared name not builtin: get_ia_param
Error compiling Cython file:
------------------------------------------------------------
...
# Handle the case of shift="auto"
if self._params["shift"]=="auto":
# Calc shift
self._params["shift"]= -( (self._params["sigma"]/self._params["cutoff"])**12 - (self._params["sigma"]/self._params["cutoff"])**6 )
if lennard_jones_set_params(self._partTypes[0],self._partTypes[1],\
^
------------------------------------------------------------
interactions.pyx:174:35: undeclared name not builtin: lennard_jones_set_params
Error compiling Cython file:
------------------------------------------------------------
...
if len(key) != 2 or (not isinstance(key[0],int)) or (not isinstance(key[1],int)):
raise ValueError("NonBondedInteractions[] expects two particle types as indices.")
return NonBondedInteractionHandle(key[0],key[1])
def setForceCap(self,cap):
if forcecap_set_params(cap):
^
------------------------------------------------------------
interactions.pyx:242:25: undeclared name not builtin: forcecap_set_params
Error compiling Cython file:
------------------------------------------------------------
...
def setForceCap(self,cap):
if forcecap_set_params(cap):
raise Exception("Could not set forcecap")
def getForceCap(self):
return force_cap
^
------------------------------------------------------------
interactions.pyx:246:20: undeclared name not builtin: force_cap
Error compiling Cython file:
------------------------------------------------------------
...
Or called with keyword arguments describing a new interaction."""
# Interaction id as argument
if len(args)==1 and isinstance(args[0],int):
bondId=args[0]
# Check, if the bond in Espresso core is really defined as a FENE bond
if bonded_ia_params[bondId].type != self.typeNumber():
^
------------------------------------------------------------
interactions.pyx:262:25: undeclared name not builtin: bonded_ia_params
Error compiling Cython file:
------------------------------------------------------------
...
{"k":bonded_ia_params[self._bondId].p.fene.k,\
"d_r_max":bonded_ia_params[self._bondId].p.fene.drmax,\
"r_0":bonded_ia_params[self._bondId].p.fene.r0}
def _setParamsInEsCore(self):
fene_set_params(self._bondId,self._params["k"],self._params["d_r_max"],self._params["r_0"])
^
------------------------------------------------------------
interactions.pyx:376:19: undeclared name not builtin: fene_set_params
Error compiling Cython file:
------------------------------------------------------------
...
{"k":bonded_ia_params[self._bondId].p.harmonic.k,\
"r_0":bonded_ia_params[self._bondId].p.harmonic.r,\
"r_cut":bonded_ia_params[self._bondId].p.harmonic.r_cut}
def _setParamsInEsCore(self):
harmonic_set_params(self._bondId,self._params["k"],self._params["r_0"],self._params["r_cut"])
^
------------------------------------------------------------
interactions.pyx:402:23: undeclared name not builtin: harmonic_set_params
Error compiling Cython file:
------------------------------------------------------------
...
{"mult":bonded_ia_params[self._bondId].p.dihedral.mult,\
"bend":bonded_ia_params[self._bondId].p.dihedral.bend,\
"phase":bonded_ia_params[self._bondId].p.dihedral.phase}
def _setParamsInEsCore(self):
dihedral_set_params(self._bondId,self._params["mult"],self._params["bend"],self._params["phase"])
^
------------------------------------------------------------
interactions.pyx:428:23: undeclared name not builtin: dihedral_set_params
Error compiling Cython file:
------------------------------------------------------------
...
"minval":bonded_ia_params[self._bondId].p.tab.minval,\
"maxval":bonded_ia_params[self._bondId].p.tab.maxval,\
"invstepsize":bonded_ia_params[self._bondId].p.tab.invstepsize}
def _setParamsInEsCore(self):
tabulated_bonded_set_params(self._bondId, self._params["type"], self._params["filename"])
^
------------------------------------------------------------
interactions.pyx:459:33: undeclared name not builtin: tabulated_bonded_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"k":bonded_ia_params[self._bondId].p.subt_lj.k,\
"r":bonded_ia_params[self._bondId].p.subt_lj.r}
def _setParamsInEsCore(self):
subt_lj_set_params(self._bondId,self._params["k"],self._params["r"])
^
------------------------------------------------------------
interactions.pyx:508:22: undeclared name not builtin: subt_lj_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"bend":bonded_ia_params[self._bondId].p.angle_harmonic.bend,\
"phi0":bonded_ia_params[self._bondId].p.angle_harmonic.phi0}
def _setParamsInEsCore(self):
angle_harmonic_set_params(self._bondId,self._params["bend"],self._params["phi0"])
^
------------------------------------------------------------
interactions.pyx:684:29: undeclared name not builtin: angle_harmonic_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"bend":bonded_ia_params[self._bondId].p.angle_cosine.bend,\
"phi0":bonded_ia_params[self._bondId].p.angle_cosine.phi0}
def _setParamsInEsCore(self):
angle_cosine_set_params(self._bondId,self._params["bend"],self._params["phi0"])
^
------------------------------------------------------------
interactions.pyx:709:27: undeclared name not builtin: angle_cosine_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"bend":bonded_ia_params[self._bondId].p.angle_cossquare.bend,\
"phi0":bonded_ia_params[self._bondId].p.angle_cossquare.phi0}
def _setParamsInEsCore(self):
angle_cossquare_set_params(self._bondId,self._params["bend"],self._params["phi0"])
^
------------------------------------------------------------
interactions.pyx:734:30: undeclared name not builtin: angle_cossquare_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"r0":bonded_ia_params[self._bondId].p.stretching_force.r0,\
"ks":bonded_ia_params[self._bondId].p.stretching_force.ks}
def _setParamsInEsCore(self):
stretching_force_set_params(self._bondId,self._params["r0"],self._params["ks"])
^
------------------------------------------------------------
interactions.pyx:759:31: undeclared name not builtin: stretching_force_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"A0_l":bonded_ia_params[self._bondId].p.area_force_local.A0_l,\
"ka_l":bonded_ia_params[self._bondId].p.area_force_local.ka_l}
def _setParamsInEsCore(self):
area_force_local_set_params(self._bondId,self._params["A0_l"],self._params["ka_l"])
^
------------------------------------------------------------
interactions.pyx:784:31: undeclared name not builtin: area_force_local_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"phi0":bonded_ia_params[self._bondId].p.bending_force.phi0,\
"kb":bonded_ia_params[self._bondId].p.bending_force.kb}
def _setParamsInEsCore(self):
bending_force_set_params(self._bondId,self._params["phi0"],self._params["kb"])
^
------------------------------------------------------------
interactions.pyx:809:28: undeclared name not builtin: bending_force_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"V0":bonded_ia_params[self._bondId].p.volume_force.V0,\
"kv":bonded_ia_params[self._bondId].p.volume_force.kv}
def _setParamsInEsCore(self):
volume_force_set_params(self._bondId,self._params["V0"],self._params["kv"])
^
------------------------------------------------------------
interactions.pyx:834:27: undeclared name not builtin: volume_force_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"A0_g":bonded_ia_params[self._bondId].p.area_force_global.A0_g,\
"ka_g":bonded_ia_params[self._bondId].p.area_force_global.ka_g}
def _setParamsInEsCore(self):
area_force_global_set_params(self._bondId,self._params["A0_g"],self._params["ka_g"])
^
------------------------------------------------------------
interactions.pyx:859:32: undeclared name not builtin: area_force_global_set_params
Error compiling Cython file:
------------------------------------------------------------
...
return \
{"r0":bonded_ia_params[self._bondId].p.stretchlin_force.r0,\
"kslin":bonded_ia_params[self._bondId].p.stretchlin_force.kslin}
def _setParamsInEsCore(self):
stretchlin_force_set_params(self._bondId,self._params["r0"],self._params["kslin"])
^
------------------------------------------------------------
interactions.pyx:884:31: undeclared name not builtin: stretchlin_force_set_params
make[4]: *** [interactions.cpp] Error 1
make[4]: Leaving directory `/home/harmanjit/espresso-master/src/python/espressomd'
make[3]: *** [all] Error 2
make[3]: Leaving directory `/home/harmanjit/espresso-master/src/python/espressomd'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/harmanjit/espresso-master/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/harmanjit/espresso-master/src'
make: *** [all-recursive] Error 1
On Thu, Feb 26, 2015 at 2:52 AM, Georg Rempfer <address@hidden> wrote:
Closed #211.
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On Thu, Feb 26, 2015 at 2:36 AM, Michael Kuron <address@hidden> wrote:
These commits are not ready for merging. They (I assume inadvertedly) revert parts of recent commits in the files you edited and likely don't compile. Please make sure you base your edits on the current master and resubmit.
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