Commit 4d4cb98b authored by Berk Onat's avatar Berk Onat

Update Gromacs parser to fit new functions in SmartParser

parent fccd5834
Pipeline #23836 failed with stage
in 7 minutes and 25 seconds
......@@ -28,12 +28,12 @@ def get_fileListDict():
infoPurpose=['trajectory', 'unitcell'], matchNames="-o"),
'traj_compxtc' : FileInfoMap(startpage, fileFormat=['.xtc', '.xdr'],
infoPurpose=['trajectory', 'unitcell'], matchNames="-x"),
'statecpt' : FileInfoMap(startpage, activeInfo=True, fileFormat=['.cpt'],
infoPurpose=['inputcoordinates', 'inputvelocities', 'inputunitcell'],
matchNames="-cpi"),
'confoutgro' : FileInfoMap(startpage, activeInfo=True, fileFormat=['.gro', '.g96', '.pdb'],
infoPurpose=['inputcoordinates', 'inputvelocities', 'inputunitcell'],
matchNames="-c"),
#'statecpt' : FileInfoMap(startpage, activeInfo=True, fileFormat=['.cpt'],
# infoPurpose=['inputcoordinates', 'inputvelocities', 'inputunitcell'],
# matchNames="-cpi"),
#'confoutgro' : FileInfoMap(startpage, activeInfo=True, fileFormat=['.gro', '.g96', '.pdb'],
# infoPurpose=['inputcoordinates', 'inputvelocities', 'inputunitcell'],
# matchNames="-c"),
'eneredr' : FileInfoMap(startpage, activeInfo=True, fileFormat=['.edr'],
infoPurpose=['thermostats'], matchNames="-e"),
'mdlog' : FileInfoMap(startpage),
......@@ -123,7 +123,7 @@ def get_nameListDict(self, deflist):
cntrllist = {
'integrator' : MetaInfoMap(startpage, defaultValue=''),
'tinit' : MetaInfoMap(startpage, defaultValue=0),
'dt' : MetaInfoMap(startpage, defaultValue=0.001),
'dt' : MetaInfoMap(startpage, defaultValue=0.0001),
'nsteps' : MetaInfoMap(startpage, defaultValue=0),
'init-step' : MetaInfoMap(startpage, defaultValue=0),
'simulation-part' : MetaInfoMap(startpage, defaultValue=0),
......@@ -368,12 +368,18 @@ def get_nameListDict(self, deflist):
'Time' : MetaInfoMap(startpage),
'Lambda' : MetaInfoMap(startpage),
'Bond' : MetaInfoMap(startpage),
'Angle' : MetaInfoMap(startpage),
'G96Bond' : MetaInfoMap(startpage),
'G96Angle' : MetaInfoMap(startpage),
'U-B' : MetaInfoMap(startpage),
'Proper Dih.' : MetaInfoMap(startpage),
'Improper Dih.' : MetaInfoMap(startpage),
'CMAP Dih.' : MetaInfoMap(startpage),
'LJ (SR)' : MetaInfoMap(startpage),
'LJ (LR)' : MetaInfoMap(startpage),
'Disper. corr.' : MetaInfoMap(startpage),
'Coulomb (SR)' : MetaInfoMap(startpage),
'Coul. recip.' : MetaInfoMap(startpage),
'LJ-14' : MetaInfoMap(startpage),
'Coulomb-14' : MetaInfoMap(startpage),
'Potential' : MetaInfoMap(startpage),
......@@ -381,8 +387,10 @@ def get_nameListDict(self, deflist):
'Total Energy' : MetaInfoMap(startpage),
'Conserved En.' : MetaInfoMap(startpage),
'Temperature' : MetaInfoMap(startpage),
'Pres. DC (bar)' : MetaInfoMap(startpage),
'Pressure (bar)' : MetaInfoMap(startpage),
'Constr. rmsd' : MetaInfoMap(startpage),
'dVremain/dl' : MetaInfoMap(startpage),
'Virial-Tensor' : MetaInfoMap(startpage),
'Pressure-Tensor' : MetaInfoMap(startpage),
}
......@@ -395,12 +403,18 @@ def get_nameListDict(self, deflist):
edrdatalist = {
'Time' : MetaInfoMap(startpage),
'Bond' : MetaInfoMap(startpage),
'Angle' : MetaInfoMap(startpage),
'G96Bond' : MetaInfoMap(startpage),
'G96Angle' : MetaInfoMap(startpage),
'U-B' : MetaInfoMap(startpage),
'Proper Dih.' : MetaInfoMap(startpage),
'Improper Dih.' : MetaInfoMap(startpage),
'CMAP Dih.' : MetaInfoMap(startpage),
'LJ (SR)' : MetaInfoMap(startpage),
'LJ (LR)' : MetaInfoMap(startpage),
'Disper. corr.' : MetaInfoMap(startpage),
'Coulomb (SR)' : MetaInfoMap(startpage),
'Coul. recip.' : MetaInfoMap(startpage),
'LJ-14' : MetaInfoMap(startpage),
'Coulomb-14' : MetaInfoMap(startpage),
'Potential' : MetaInfoMap(startpage),
......@@ -408,8 +422,10 @@ def get_nameListDict(self, deflist):
'Total Energy' : MetaInfoMap(startpage),
'Conserved En.' : MetaInfoMap(startpage),
'Temperature' : MetaInfoMap(startpage),
'Pres. DC (bar)' : MetaInfoMap(startpage),
'Pressure (bar)' : MetaInfoMap(startpage),
'Constr. rmsd' : MetaInfoMap(startpage),
'dVremain/dl' : MetaInfoMap(startpage),
'Virial-Tensor' : MetaInfoMap(startpage),
'Pressure-Tensor' : MetaInfoMap(startpage),
}
......@@ -1007,7 +1023,8 @@ def get_updateDictionary(self, defname):
lookupdict=self.mddataDict
),
'frame_sequence_temperature_frames' : MetaInfoMap(startpage,
depends=[{'store' : 'Step'}],
depends=[{'test' : [['Volume', ' is not None']],
'store' : 'Step'}],
valtype='int',
lookupdict=self.mddataDict
),
......@@ -1028,7 +1045,8 @@ def get_updateDictionary(self, defname):
),
'x_gromacs_frame_sequence_volume_frames' : MetaInfoMap(startpage,
activeSections=['section_frame_sequence'],
depends=[{'store' : 'Step'}],
depends=[{'test' : [['Volume', ' is not None']],
'store' : 'Step'}],
valtype='int',
lookupdict=self.mddataDict
),
......
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