From 8fd1c65a8fa012bd64277cad40d62dbfa1ec46b9 Mon Sep 17 00:00:00 2001 From: CHerfarth Date: Tue, 16 Sep 2025 11:40:00 +0300 Subject: [PATCH 1/2] updated regexes and failcheck for delphi --- biskit/exe/delphi.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/biskit/exe/delphi.py b/biskit/exe/delphi.py index 6fd3cd31..381a3e58 100644 --- a/biskit/exe/delphi.py +++ b/biskit/exe/delphi.py @@ -291,11 +291,11 @@ class Delphi( Executor ): 'all_aminont03.in', 'all_nuc02.in' ] - RE_E_GRID = r'total grid energy\s+:\s+(?P[0-9\-\.]+)\s+kt' - RE_E_COUL = r'coulombic energy\s+:\s+(?P[0-9\-\.]+)\s+kt' - RE_E_SELF = r'self-reaction field energy\s+:\s+(?P[0-9\-\.]+)\s+kt' - RE_E_RXN = r'corrected reaction field energy\s*:\s+(?P[0-9\-\.]+)\s+kt' - RE_E_RXNT = r'total reaction field energy\s*:\s+(?P[0-9\-\.]+)\s+kt' + RE_E_GRID = r'Energy> Total grid energy\s+:\s+(?P[0-9\-\.]+)\s+kT' + RE_E_COUL = r'Energy> Coulombic energy\s+:\s+(?P[0-9\-\.]+)\s+kT' + RE_E_SELF = r'self-reaction field energy\s+:\s+(?P[0-9\-\.]+)\s+kT' + RE_E_RXN = r'Energy> Corrected reaction field energy\s*:\s+(?P[0-9\-\.]+)\s+kT' + RE_E_RXNT = r'total reaction field energy\s*:\s+(?P[0-9\-\.]+)\s+kT' RE_SURFCH = r'total s\.charge\,no epsin carrying\s*:\s+(?P[0-9\-\.]+)' @@ -582,7 +582,7 @@ def isFailed( self ): Overrides Executor method """ return self.output is None or \ - not 'energy calculations done' in self.output + not 'PROGRAM EXITS SUCCESSFULLY' in self.output def fail( self ): """ @@ -593,7 +593,7 @@ def fail( self ): self.log.add( s ) if self.output: s = 'The last message from DelPhi reads as follows:\n' - s += '\n'.join( self.output.split('\n')[-3:] ) + s += '\n'.join( self.output.split('\n')[-300:] ) self.log.add( s ) else: self.log.add( 'There does not seem to be any DelPhi output.') From fa952c042cc33731aef108017fb69cdfd1529d6a Mon Sep 17 00:00:00 2001 From: CHerfarth Date: Tue, 16 Sep 2025 11:44:14 +0300 Subject: [PATCH 2/2] removed missing energy vals --- biskit/exe/delphi.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/biskit/exe/delphi.py b/biskit/exe/delphi.py index 381a3e58..2b073ed0 100644 --- a/biskit/exe/delphi.py +++ b/biskit/exe/delphi.py @@ -293,10 +293,12 @@ class Delphi( Executor ): RE_E_GRID = r'Energy> Total grid energy\s+:\s+(?P[0-9\-\.]+)\s+kT' RE_E_COUL = r'Energy> Coulombic energy\s+:\s+(?P[0-9\-\.]+)\s+kT' - RE_E_SELF = r'self-reaction field energy\s+:\s+(?P[0-9\-\.]+)\s+kT' RE_E_RXN = r'Energy> Corrected reaction field energy\s*:\s+(?P[0-9\-\.]+)\s+kT' - RE_E_RXNT = r'total reaction field energy\s*:\s+(?P[0-9\-\.]+)\s+kT' - RE_SURFCH = r'total s\.charge\,no epsin carrying\s*:\s+(?P[0-9\-\.]+)' + #Note: These are energy values not in the output of Delphi v8 anymore. + #Programs relying on these energy terms will fail + #RE_E_SELF = r'self-reaction field energy\s+:\s+(?P[0-9\-\.]+)\s+kT' + #RE_E_RXNT = r'total reaction field energy\s*:\s+(?P[0-9\-\.]+)\s+kT' + #RE_SURFCH = r'total s\.charge\,no epsin carrying\s*:\s+(?P[0-9\-\.]+)' def __init__( self, @@ -617,8 +619,7 @@ def parseOutput( self ): Assumes output file has been parsed into self.output """ r = {} - for pattern in [self.RE_E_COUL, self.RE_E_GRID, self.RE_E_RXN, - self.RE_E_SELF, self.RE_E_RXNT, self.RE_SURFCH]: + for pattern in [self.RE_E_COUL, self.RE_E_GRID, self.RE_E_RXN, ]: ex = re.compile( pattern ) hit = ex.search( self.output ) try: