This is TeX, Version 3.14159 (Web2C 7.3.1) (format=latex 2001.3.24) 4 OCT 2001 07:46 **refman.tex (refman.tex LaTeX2e <2000/06/01> Babel and hyphenation patterns for american, french, german, ngerman, i talian, portuges, spanish, swedish, nohyphenation, loaded. (/usr/share/texmf/tex/latex/base/book.cls Document Class: book 2000/05/19 v1.4b Standard LaTeX document class (/usr/share/texmf/tex/latex/base/bk10.clo File: bk10.clo 2000/05/19 v1.4b Standard LaTeX file (size option) ) \c@part=\count79 \c@chapter=\count80 \c@section=\count81 \c@subsection=\count82 \c@subsubsection=\count83 \c@paragraph=\count84 \c@subparagraph=\count85 \c@figure=\count86 \c@table=\count87 \abovecaptionskip=\skip41 \belowcaptionskip=\skip42 \bibindent=\dimen102 ) (/usr/share/texmf/tex/latex/misc/a4wide.sty Package: a4wide 1994/08/30 (/usr/share/texmf/tex/latex/ntgclass/a4.sty Package: a4 1999/03/03 v1.2f A4 based page layout )) (/usr/share/texmf/tex/latex/base/makeidx.sty Package: makeidx 2000/03/29 v1.0m Standard LaTeX package ) (/usr/share/texmf/tex/latex/fancyhdr/fancyhdr.sty \headwidth=\dimen103 ) (/usr/share/texmf/tex/latex/graphics/graphicx.sty Package: graphicx 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR) (/usr/share/texmf/tex/latex/graphics/keyval.sty Package: keyval 1999/03/16 v1.13 key=value parser (DPC) \KV@toks@=\toks14 ) (/usr/share/texmf/tex/latex/graphics/graphics.sty Package: graphics 1999/02/16 v1.0l Standard LaTeX Graphics (DPC,SPQR) (/usr/share/texmf/tex/latex/graphics/trig.sty Package: trig 1999/03/16 v1.09 sin cos tan (DPC) ) (/usr/share/texmf/tex/latex/config/graphics.cfg) Package graphics Info: Driver file: dvips.def on input line 80. (/usr/share/texmf/tex/latex/graphics/dvips.def File: dvips.def 1999/02/16 v3.0i Driver-dependant file (DPC,SPQR) )) \Gin@req@height=\dimen104 \Gin@req@width=\dimen105 ) (/usr/share/texmf/tex/latex/misc/float.sty Package: float 1999/05/29 v1.2d Float enhancements (AL) \c@float@type=\count88 \float@box=\box26 \@floatcapt=\box27 ) (/usr/share/texmf/tex/latex/base/alltt.sty Package: alltt 1997/06/16 v2.0g defines alltt environment ) (doxygen.sty Package: doxygen (/usr/share/texmf/tex/latex/tools/calc.sty Package: calc 1998/07/07 v4.1b Infix arithmetic (KKT,FJ) \calc@Acount=\count89 \calc@Bcount=\count90 \calc@Adimen=\dimen106 \calc@Bdimen=\dimen107 \calc@Askip=\skip43 \calc@Bskip=\skip44 LaTeX Info: Redefining \setlength on input line 59. LaTeX Info: Redefining \addtolength on input line 60. \calc@denominator=\count91 ) (/usr/share/texmf/tex/latex/tools/array.sty Package: array 1998/05/13 v2.3m Tabular extension package (FMi) \col@sep=\dimen108 \extrarowheight=\dimen109 \NC@list=\toks15 \extratabsurround=\skip45 \backup@length=\skip46 ) \tmplength=\skip47 ) \@indexfile=\write3 \openout3 = `refman.idx'. Writing index file refman.idx (refman.aux (class_AMatrix.aux) (class_AMatrix__AMatrixRep.aux) (class_AnimFrame.aux) (class_Atom.aux) (class_AtomBuildup.aux) (class_AtomConstraint.aux) (class_AtomRegistry.aux) (class_base_iterator.aux) (class_bf_iterator.aux) (class_BinEnvelopeConstraint.aux) (class_ConstIterator.aux) (class_Constraint.aux) (class_ConstraintManager.aux) (class_ConstraintRegistry.aux) (class_CycleAll.aux) (class_ddEdge.aux) (class_ddGraph.aux) (class_ddVertex.aux) (class_df_iterator.aux) (class_DistanceConstraint.aux) (class_DLList.aux) (class_DLListNode.aux) (class_DLListRep.aux) (class_DSIterator.aux) (class_DynString.aux) (class_Envelope.aux) (class_EnvelopeConstraint.aux) (class_Grid.aux) (class_gwNumerics.aux) (class_gwRelaxAtom.aux) (class_IdGen.aux) (class_IntPriorityQueue.aux) (class_IntVec.aux) (class_Iterator.aux) (class_ABitSet__Iterator.aux) (class_jdErr_Eval.aux) (class_jdIterator.aux) (class_jdOcc_Count.aux) (class_jdRand_Eval.aux) (class_jVector.aux) (class_KAdjMat.aux) (class_Matrix.aux) (class_Molecule.aux) (class_neighbor_iterator.aux) (class_path_iterator.aux) (class_PositionConstraint.aux) (class_Process.aux) (class_Queue.aux) (class_RanBaseClass.aux) (class_RanChar.aux) (class_RanDbl.aux) (class_RanInt.aux) (class_RanLetter.aux) (class_RanWord.aux) (class_RefRep.aux) (class_RelaxSubset.aux) (class_Residue.aux) (class_ResidueRegistry.aux) (class_SatisfyMolecule.aux) (class_sdEdge.aux) (class_sdGraph.aux) (class_sdVertex.aux) (class_Segment.aux) (class_Segments.aux) (class_Stack.aux) (class_StopEval.aux) (class_UnitWeight.aux) (class_z.aux) (abitset_C.aux) (abitset_h.aux) (ajiobin_h.aux) (amatrix_h.aux) (amatrix_inc.aux) (atom_h.aux) (atom_buildup_C.aux) (atom_buildup_h.aux) (atom_constraint_C.aux) (atom_constraint_h.aux) (atom_registry_C.aux) (atom_registry_h.aux) (bin_envelope_constraint_C.aux) (bin_envelope_constraint_h.aux) (bits_h.aux) (compoper_h.aux) (constraint_C.aux) (constraint_h.aux) (constraint_manager_C.aux) (constraint_manager_h.aux) (constraint_registry_C.aux) (constraint_registry_h.aux) (cycle_all_C.aux) (cycle_all_h.aux) (ddgraph_h.aux) (ddgraph_inc.aux) (ddvertex_h.aux) (ddvertex_inc.aux) (dens-trans_C.aux) (dist_C.aux) (distance_constraint_C.aux) (distance_constraint_h.aux) (dllist_h.aux) (dllist_inc.aux) (dlliter_inc.aux) (dsiter_inc.aux) (dynstring_C.aux) (dynstring_h.aux) (env_diff_C.aux) (envelope_C.aux) (envelope_h.aux) (envelope_constraint_C.aux) (envelope_constraint_h.aux) (err_eval_C.aux) (error_handler_h.aux) (globals_C.aux) (globals_h.aux) (grape_C.aux) (graph_weights_h.aux) (grid_C.aux ) (grid_h.aux) (gw_numerics_C.aux) (gw_numerics_h.aux) (gw_relax_atom_C.aux) (gw_relax_atom_h.aux) (idgen_h.aux) (intvec_C.aux) (intvec_h.aux) (intvec_inc.aux) (ipqueue_h.aux) (ipqueue_inc.aux) (jd_anim_frame_C.aux) (jd_anim_frame_h.aux) (jd_err_eval_C.aux) (jd_err_eval_h.aux) (jd_iterator_C.aux) (jd_iterator_h.aux) (jd_occ_count_C.aux) (jd_occ_count_h.aux) (jd_rand_eval_C.aux) (jd_rand_eval_h.aux) (jd_relax_subset_C.aux) (jd_relax_subset_h.aux) (jd_stop_eval_C.aux) (jd_stop_eval_h.aux) (jsmisc_h.aux) (jvector_C.aux) (jvector_h.aux) (kadjmat_h.aux) (LeakTracer_Makefile.aux) (lib_Makefile.aux) (Makefile.aux) (src_aux_Makefile.aux) (src_Makefile.aux) (matrix_C.aux) (matrix_h.aux) (molecule_C.aux) (molecule_h.aux) (molio_C.aux) (ocount_C.aux) (position_constraint_C.aux) (position_constraint_h.aux) (process_C.aux) (process_h.aux) (queue_h.aux) (rand_eval_C.aux) (randomgenerator_C.aux) (randomgenerator_h.aux) (refrep_h.aux) (residue_C.aux) (residue_h.aux) (residue_registry_h.aux) (satisfy_molecule_h.aux) (sdgalg_inc.aux) (sdgiter_inc.aux) (sdgraph_h.aux) (sdgraph_inc.aux) (sdvertex_h.aux) (sdvertex_inc.aux) (search-sort_h.aux) (segments_inc.aux) (stack_h.aux) (streamoper_h.aux) (top_process_h.aux) (utils_C.aux) (utils_h.aux)) \openout1 = `refman.aux'. LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 12. LaTeX Font Info: ... okay on input line 12. [1 ] [2 ] (refman.toc LaTeX Font Info: External font `cmex10' loaded for size (Font) <7> on input line 2. LaTeX Font Info: External font `cmex10' loaded for size (Font) <5> on input line 2. [1 ] Underfull \vbox (badness 1389) has occurred while \output is active [] LaTeX Font Info: Try loading font information for OMS+cmr on input line 1579 . (/usr/share/texmf/tex/latex/base/omscmr.fd File: omscmr.fd 1999/05/25 v2.5h Standard LaTeX font definitions ) LaTeX Font Info: Font shape `OMS/cmr/bx/n' in size <7> not available (Font) Font shape `OMS/cmsy/b/n' tried instead on input line 1579. [2] [3] Underfull \vbox (badness 1389) has occurred while \output is active [] [4] Underfull \vbox (badness 1389) has occurred while \output is active [] [5]) \tf@toc=\write4 \openout4 = `refman.toc'. [6] Chapter 1. (hierarchy.tex [1 ]) [2] Chapter 2. (annotated.tex [3 ]) [4] Chapter 3. (files.tex [5 ] [6]) [7] [8 ] Chapter 4. (class_ABitSet.tex LaTeX Font Info: Font shape `OMS/cmr/m/n' in size <10> not available (Font) Font shape `OMS/cmsy/m/n' tried instead on input line 8. [9] [10] [11] [12] [13] [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 503--503 []\OT1/cmr/m/n/10 Referenced by Add(), KAdj-Mat::Connect(), Set(), bf[]-iterato r::operator++(), df[]- [] [16] [17] [18] [19]) [20] \openout2 = `class_AMatrix.aux'. (class_AMatrix.tex File: class_AMatrix_coll_graph.eps Graphic file (type eps) [21 ] [22] Underfull \hbox (badness 10000) in paragraph at lines 248--248 [] [23] Underfull \hbox (badness 10000) in paragraph at lines 278--278 [] [24] Underfull \hbox (badness 1248) in paragraph at lines 370--370 []\OT1/cmr/m/n/10 Referenced by op-er-a-tor!=(), operator$\OML/cmm/m/it/10 <$\O T1/cmr/m/n/10 (), operator$\OML/cmm/m/it/10 <$\OT1/cmr/m/n/10 =(), op-er-a-tor= =(), operator$\OML/cmm/m/it/10 >$\OT1/cmr/m/n/10 (), and [] [25] Underfull \vbox (badness 4467) has occurred while \output is active [] [26] [27] [28] [29] [30] [31] [32] [33] [34]) [35] \openout2 = `class_AMatrix__AMatrixRep.aux'. (class_AMatrix__AMatrixRep.tex File: class_AMatrix__AMatrixRep_inherit_graph.eps Graphic file (type eps) File: class_AMatrix__AMatrixRep_coll_graph.eps Graphic file (type eps) [36 ] [37]) [38] \openout2 = `class_AnimFrame.aux'. (class_AnimFrame.tex File: class_AnimFrame_inherit_graph.eps Graphic file (type eps) File: class_AnimFrame_coll_graph.eps Graphic file (type eps) [39 ] [40] [41]) [42] \openout2 = `class_Atom.aux'. (class_Atom.tex File: class_Atom_coll_graph.eps Graphic file (type eps) [43 ] [44] [45] [46] [47] [48]) [49] \openout2 = `class_AtomBuildup.aux'. (class_AtomBuildup.tex File: class_AtomBuildup_inherit_graph.eps Graphic file (type eps) File: class_AtomBuildup_coll_graph.eps Graphic file (type eps) [50 ] [51] [52] [53]) [54] \openout2 = `class_AtomConstraint.aux'. (class_AtomConstraint.tex File: class_AtomConstraint_inherit_graph.eps Graphic file (type eps) File: class_AtomConstraint_coll_graph.eps Graphic file (type eps) [55 ] [56] [57] Overfull \hbox (85.82108pt too wide) in paragraph at lines 210--210 []\OT1/cmtt/m/n/8 00045 DIE("Tried to computeStress' on atom constraint for an atom other than the one pointed to by the constraint");[] [] [58] Overfull \hbox (77.32095pt too wide) in paragraph at lines 262--262 []\OT1/cmtt/m/n/8 00058 DIE("Tried to call dStress on atom constraint for a n atom other than the one pointed to by its constraint");[] [] [59]) [60] \openout2 = `class_AtomRegistry.aux'. (class_AtomRegistry.tex Overfull \hbox (22.07016pt too wide) in paragraph at lines 45--45 []\OT1/cmtt/m/n/8 00054 { [] Overfull \hbox (102.82132pt too wide) in paragraph at lines 45--45 []\OT1/cmtt/m/n/8 00058 if (a.Type().Length() > 0) {cerr <<"|"<< a.Type() <<"|" < File: class_base_iterator_coll_graph.eps Graphic file (type eps) [63 ] [64] [65]) [66] \openout2 = `class_bf_iterator.aux'. (class_bf_iterator.tex File: class_bf_iterator_inherit_graph.eps Graphic file (type eps) File: class_bf_iterator_coll_graph.eps Graphic file (type eps) [67 ] [68] [69]) [70] \openout2 = `class_BinEnvelopeConstraint.aux'. (class_BinEnvelopeConstraint.tex File: class_BinEnvelopeConstraint_inherit_graph.eps Graphic file (type eps) File: class_BinEnvelopeConstraint_coll_graph.eps Graphic file (type eps) [71 ] [72] [73] Overfull \hbox (13.57004pt too wide) in paragraph at lines 189--189 []\OT1/cmtt/m/n/8 00022 myType = BinEnvelopeConstraint::Identifier; // needs to be done here -- not read in by registry[] [] [74] Overfull \hbox (26.32022pt too wide) in paragraph at lines 267--267 []\OT1/cmtt/m/n/8 00042 double rv = util_max(0.,(MAX_ENV_DEN-(EC->getDensity( getMolecule()(supportA[0]))))/ENV_DEN_RANGE);[] [] [75]) [76] \openout2 = `class_ConstIterator.aux'. (class_ConstIterator.tex File: class_ConstIterator_coll_graph.eps Graphic file (type eps) [77 ] [78]) [79] \openout2 = `class_Constraint.aux'. (class_Constraint.tex File: class_Constraint_inherit_graph.eps Graphic file (type eps) File: class_Constraint_coll_graph.eps Graphic file (type eps) [80 ] Underfull \hbox (badness 10000) in paragraph at lines 88--90 []\OT1/cmr/bx/n/10 Constraint \OT1/cmr/m/n/10 (\OT1/cmr/bx/n/10 Constraint-Man ager \OT1/cmr/m/n/10 &cm, const \OT1/cmr/bx/n/10 Int-Vec \OT1/cmr/m/n/10 &suppo rt-AIndices=\OT1/cmr/bx/n/10 Int- [] [81] [82] Underfull \vbox (badness 1502) has occurred while \output is active [] [83] [84] [85] Overfull \hbox (111.32144pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/8 00425 printf ("Constraint::addAtomSupport-> added atom su pport from constraint %d to %d\n SHOULD THIS OCCUR?", myID, Id );[] [] Overfull \hbox (107.07138pt too wide) in paragraph at lines 386--386 []\OT1/cmtt/m/n/8 00438 // printf ("Constraint::addConstraintSupport-> a dded constraint support from constraint %d to %d\n", myID, Id );[] [] [86] Overfull \hbox (56.07065pt too wide) in paragraph at lines 515--515 []\OT1/cmtt/m/n/8 00343 <<"). I'm trying to validate my suppo rts => now I call assertValidity on " << child->myID[] [] [87] [88] [89] Underfull \hbox (badness 10000) in paragraph at lines 598--598 []\OT1/cmr/m/n/10 Referenced by Distance-Constraint::compute-Abs-Res(), Positio n-Constraint::compute-Stress(), [] Underfull \hbox (badness 1308) in paragraph at lines 598--598 \OT1/cmr/m/n/10 Distance-Constraint::compute-Stress(), Bin-Envelope-Constraint: :compute-Stress(), and Distance- [] Overfull \hbox (34.82034pt too wide) in paragraph at lines 661--661 []\OT1/cmtt/m/n/8 00261 DIE ("This should not be called -- instead, atoms should turn off constraints when turned off");[] [] [90] [91] [92] Underfull \hbox (badness 10000) in paragraph at lines 782--782 []\OT1/cmr/m/n/10 Referenced by Constraint-Manager::Turn-Atom-On(), Constraint- Manager::Turn-Atoms-Off(), [] [93] Underfull \vbox (badness 10000) has occurred while \output is active [] [94] [95]) [96] \openout2 = `class_ConstraintManager.aux'. (class_ConstraintManager.tex File: class_ConstraintManager_coll_graph.eps Graphic file (type eps) [97 ] [98] [99] [100] [101] [102] [103] Underfull \hbox (badness 5008) in paragraph at lines 453--453 []\OT1/cmr/m/n/10 Referenced by Constraint-Manager(), Con-straint::Input(), Con straint::Input-Binary(), and [] [104] [105] [106] [107] [108] Underfull \hbox (badness 10000) in paragraph at lines 781--781 []\OT1/cmr/m/n/10 Referenced by Print-Graph(), Constraint::assert-Validity(), C onstraint::switch-Off(), and [] [109] [110] Overfull \hbox (22.07016pt too wide) in paragraph at lines 883--883 []\OT1/cmtt/m/n/8 00276 {M.readXmol(is);InvalidateAtoms();} [] Underfull \hbox (badness 2503) in paragraph at lines 902--902 []\OT1/cmr/m/n/10 Referenced by Con-straint::Input(), Constraint::Input-Binary( ), clear-All-Constraints(), clear- [] [111] [112] [113] [114]) [115] \openout2 = `class_ConstraintRegistry.aux'. (class_ConstraintRegistry.tex [116 ] [117]) [118] \openout2 = `class_CycleAll.aux'. (class_CycleAll.tex File: class_CycleAll_inherit_graph.eps Graphic file (type eps) File: class_CycleAll_coll_graph.eps Graphic file (type eps) [119 ] [120] Overfull \hbox (56.07065pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/8 00044 cerr << setprecision(50) << "ORDER: \t" << "Ma xAbsDistRes = "<< gwNumerics::MaxAbsDistRes << endl;[] [] Overfull \hbox (64.57077pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/8 00061 cerr << setprecision(50) << "Set ORDER: \t" << "Priority for atom " < [122 ] [123]) [124] \openout2 = `class_ddGraph.aux'. (class_ddGraph.tex File: class_ddGraph_coll_graph.eps Graphic file (type eps) [125 ] [126] [127] [128] [129] [130] [131] Underfull \hbox (badness 10000) in paragraph at lines 502--502 []\OT1/cmr/m/n/10 Referenced by sd-Graph::Copy(), Get-Data(), Constraint-Manage r::add(), Constraint- [] [132] [133] [134] [135] [136] Underfull \hbox (badness 10000) in paragraph at lines 750--750 []\OT1/cmr/m/n/10 Referenced by Constraint-Manager::Number(), Constraint-Manage r::clear-All-Constraints(), [] [137] [138] [139] [140] [141]) [142] \openout2 = `class_ddVertex.aux'. (class_ddVertex.tex [143 ] [144] [145] [146] [147] [148]) [149] \openout2 = `class_df_iterator.aux'. (class_df_iterator.tex File: class_df_iterator_inherit_graph.eps Graphic file (type eps) File: class_df_iterator_coll_graph.eps Graphic file (type eps) [150 ] [151] [152]) [153] \openout2 = `class_DistanceConstraint.aux'. (class_DistanceConstraint.tex File: class_DistanceConstraint_inherit_graph.eps Graphic file (type eps) File: class_DistanceConstraint_coll_graph.eps Graphic file (type eps) [154 ] [155] [156] [157] Overfull \hbox (17.8201pt too wide) in paragraph at lines 272--272 []\OT1/cmtt/m/n/8 00081 // cerr << "ORDER cmputstr-pos: " << Label() << ";ca lc = " << setprecision(50) << calc << endl;[] [] Overfull \hbox (13.57004pt too wide) in paragraph at lines 296--296 []\OT1/cmtt/m/n/8 00043 // cerr << "ORDER cmputstr: " << Label() << ";meas = " << setprecision(50) << measured << endl;[] [] [158] Underfull \vbox (badness 10000) has occurred while \output is active [] [159]) [160] \openout2 = `class_DLList.aux'. (class_DLList.tex File: class_DLList_inherit_graph.eps Graphic file (type eps) File: class_DLList_coll_graph.eps Graphic file (type eps) [161 ] [162] [163] [164] [165] [166] Underfull \hbox (badness 1383) in paragraph at lines 397--397 []\OT1/cmr/m/n/10 Referenced by gw-Numerics::add-VDWSegments(), Constraint-Mana ger::get-Assoc-Atoms(), and [] Underfull \hbox (badness 10000) in paragraph at lines 439--439 []\OT1/cmr/m/n/10 Referenced by Molecule::Dyn-Read(), Segments::Get-Num(), Seg- ments::Number(), Id- [] Underfull \hbox (badness 10000) in paragraph at lines 439--439 \OT1/cmr/m/n/10 Gen::Number-Free(), Output-Binary(), Segments::QSort-Reduce(), Segments::QSort-Reduce- [] Underfull \hbox (badness 1189) in paragraph at lines 439--439 \OT1/cmr/m/n/10 Viol(), Process::assert-Order(), j-Vector::dynread(), Int-Vec:: dynread(), Process::num-Queued(), [] [167] [168] Underfull \hbox (badness 5245) in paragraph at lines 527--527 []\OT1/cmr/m/n/10 Referenced by Remove-Location(), Process::assert-Order(), Pro cess::clean-Queue(), main(), [] Underfull \hbox (badness 1092) in paragraph at lines 558--558 \OT1/cmr/m/n/10 Queue::Remove(), Re-move(), Remove-Location(), j-Vector::dynrea d(), Int-Vec::dynread(), and [] [169] [170] [171] [172]) [173] \openout2 = `class_DLListNode.aux'. (class_DLListNode.tex File: class_DLListNode_coll_graph.eps Graphic file (type eps) [174 ]) [175] \openout2 = `class_DLListRep.aux'. (class_DLListRep.tex File: class_DLListRep_inherit_graph.eps Graphic file (type eps) File: class_DLListRep_coll_graph.eps Graphic file (type eps) [176 ]) [177] \openout2 = `class_DSIterator.aux'. (class_DSIterator.tex File: class_DSIterator_coll_graph.eps Graphic file (type eps) [178 ] [179] [180] [181]) [182] \openout2 = `class_DynString.aux'. (class_DynString.tex File: class_DynString_coll_graph.eps Graphic file (type eps) [183 ] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] Underfull \vbox (badness 2012) has occurred while \output is active [] [195] [196] [197] [198] [199]) [200] \openout2 = `class_Envelope.aux'. (class_Envelope.tex File: class_Envelope_coll_graph.eps Graphic file (type eps) [201 ] LaTeX Font Info: External font `cmex10' loaded for size (Font) <9> on input line 61. LaTeX Font Info: External font `cmex10' loaded for size (Font) <6> on input line 61. [202] [203] [204] [205] Overfull \hbox (102.82132pt too wide) in paragraph at lines 313--313 []\OT1/cmtt/m/n/8 00732 double * new_density_array = new double[new_numPoints ]; // not sparse -- saving lots of zeros here. mem wasted. FIX[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [206] [207] Underfull \vbox (badness 10000) has occurred while \output is active [] [208] [209] [210] Overfull \hbox (17.8201pt too wide) in paragraph at lines 581--581 []\OT1/cmtt/m/n/8 00115 cerr << "original center_of_mass: (" << r_cm_x << "," << r_cm_y << "," << r_cm_z << ")" << endl;[] [] Overfull \hbox (17.8201pt too wide) in paragraph at lines 581--581 []\OT1/cmtt/m/n/8 00128 cerr << "new center_of_mass: (" << r_cm_x << "," << r_cm_y << "," << r_cm_z << ")" << endl;[] [] [211] Overfull \hbox (17.8201pt too wide) in paragraph at lines 662--662 []\OT1/cmtt/m/n/8 00376 outStream << "totalDensity differs: " << totalDensi ty << " " << E.totalDensity << endl;[] [] Overfull \hbox (17.8201pt too wide) in paragraph at lines 662--662 []\OT1/cmtt/m/n/8 00382 outStream << "filledPoints differs: " << filledPoin ts << " " << E.filledPoints << endl;[] [] Overfull \hbox (30.57028pt too wide) in paragraph at lines 679--679 []\OT1/cmtt/m/n/8 00065 density_array = new double[numPoints]; // not sparse -- saving lots of zeros here. mem wasted. FIX[] [] [212] [213] [214] Overfull \hbox (30.57028pt too wide) in paragraph at lines 975--975 []\OT1/cmtt/m/n/8 01038 DIE("Envelope Read Error! It appears you have alrea dy read in density data into this envelope!");[] [] [215] Overfull \hbox (532.07748pt too wide) in paragraph at lines 975--975 []\OT1/cmtt/m/n/8 01103 cerr << "Envelope size error!\n\n Envelope Class us es signed ints to index data, so "<< INT_MAX << " is the maximum number of cell s possible. Your number of cells is "<< numPoints << ", which is too large."<< endl;[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [216] Overfull \hbox (73.07089pt too wide) in paragraph at lines 975--975 []\OT1/cmtt/m/n/8 01120 cerr << "Envelope reading error!\n\n read "<< readCount << " entries, expected "<< numPoints << endl;[] [] Overfull \hbox (68.82083pt too wide) in paragraph at lines 975--975 []\OT1/cmtt/m/n/8 01124 ($\ast$this)(xh,yh,zh) = val; // no t sparse -- saving lots of zeros here. mem wasted. FIX[] [] [217] Underfull \vbox (badness 10000) has occurred while \output is active [] [218] [219] Overfull \hbox (39.0704pt too wide) in paragraph at lines 1227--1227 []\OT1/cmtt/m/n/8 00885 outStream << "Material{specularColor 0.8 0. 8 0.8 diffuseColor 1 0.2 0.2 transparency 0.1" \[] [] [220] Overfull \hbox (34.82034pt too wide) in paragraph at lines 1227--1227 []\OT1/cmtt/m/n/8 00888 outStream << "Material{specularColor 0.5 0. 5 0.5 diffuseColor 0.2 0.8 0.2 transparency " \[] [] Overfull \hbox (34.82034pt too wide) in paragraph at lines 1227--1227 []\OT1/cmtt/m/n/8 00891 outStream << "Material{specularColor 0.2 0. 2 0.2 diffuseColor 0.3 0.3 0.3 transparency " \[] [] [221] Overfull \hbox (51.82059pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/8 00951 outStream << " Material{specularColor 0.8 0.8 0.8 diffuseColor 1 0.2 0.2 transparency 0.1" \[] [] Overfull \hbox (47.57053pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/8 00954 outStream << " Material{specularColor 0.5 0.5 0.5 diffuseColor 0.2 0.8 0.2 transparency " \[] [] Overfull \hbox (47.57053pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/8 00957 outStream << " Material{specularColor 0.2 0.2 0.2 diffuseColor 0.3 0.3 0.3 transparency " \[] [] Overfull \hbox (47.57053pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/8 00967 outStream << " Transform {rotation " << xr << " "<< yr << " "<< zr <<" "<< rad <<"}" << endl;[] [] Overfull \hbox (30.57028pt too wide) in paragraph at lines 1312--1312 []\OT1/cmtt/m/n/8 00969 outStream << " Scale {scaleFactor " << scal e <<" " << scale <<" " << scale <<"}" << endl;[] [] [222] [223] [224] [225] [226]) [227] \openout2 = `class_EnvelopeConstraint.aux'. (class_EnvelopeConstraint.tex File: class_EnvelopeConstraint_inherit_graph.eps Graphic file (type eps) File: class_EnvelopeConstraint_coll_graph.eps Graphic file (type eps) [228 ] [229] [230] [231] [232] [233] [234] [235] Overfull \hbox (0.81985pt too wide) in paragraph at lines 461--461 []\OT1/cmtt/m/n/8 00049 cerr << " Envelope setup failed. Envelope has " << E[0]->numPoints << " points." << endl;[] [] [236] [237] Overfull \hbox (5.06992pt too wide) in paragraph at lines 607--607 []\OT1/cmtt/m/n/8 00253 while ((i < EnvelopeConstraint::num_evelopes) && (D < EnvelopeConstraint::density_threshold))[] [] Overfull \hbox (5.06992pt too wide) in paragraph at lines 649--649 []\OT1/cmtt/m/n/8 00283 while ((i < EnvelopeConstraint::num_evelopes) && (D < EnvelopeConstraint::density_threshold))[] [] [238] [239]) [240] \openout2 = `class_Grid.aux'. (class_Grid.tex File: class_Grid_coll_graph.eps Graphic file (type eps) [241 ] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] Underfull \hbox (badness 3623) in paragraph at lines 741--741 []\OT1/cmr/m/n/10 Referenced by Molecule::Bounds(), Molecule::Copy(), Molecule: :get-COM(), Molecule::get- [] [252] [253] [254] [255] Overfull \hbox (22.07016pt too wide) in paragraph at lines 1014--1014 []\OT1/cmtt/m/n/8 00410 if (d< distance) ReturnList.AddToFront(myPoin ts[(*out_iter).second]); // jVector position[] [] Overfull \hbox (22.07016pt too wide) in paragraph at lines 1014--1014 []\OT1/cmtt/m/n/8 00425 if (d< distance) ReturnList.AddToFront(myPoin ts[(*out_iter).second]); // jVector position[] [] Overfull \hbox (30.57028pt too wide) in paragraph at lines 1070--1070 []\OT1/cmtt/m/n/8 00360 if (d< distance) ReturnList.AddToFront(myPo ints[(*out_iter).second]); // jVector position[] [] [256] Overfull \hbox (30.57028pt too wide) in paragraph at lines 1070--1070 []\OT1/cmtt/m/n/8 00377 if (d< distance) ReturnList.AddToFront(myPo ints[(*out_iter).second]); // jVector position[] [] Underfull \hbox (badness 2012) in paragraph at lines 1080--1080 []\OT1/cmr/m/n/10 Referenced by Molecule::Copy(), Molecule::Dyn-Read(), Molecul e::Input(), Molecule::Input- [] [257] Overfull \hbox (51.82059pt too wide) in paragraph at lines 1115--1115 []\OT1/cmtt/m/n/8 00239 *PointToHashIter[index_num] = GridHashMap.insert(ha shmap_type::value_type(TempGridNumber, index_num));[] [] [258] [259]) [260] \openout2 = `class_gwNumerics.aux'. (class_gwNumerics.tex Underfull \hbox (badness 2302) in paragraph at lines 21--23 []\OT1/cmr/bx/n/10 j-Vector Set-HCPosition2 \OT1/cmr/m/n/10 (const \OT1/cmr/bx /n/10 j-Vector \OT1/cmr/m/n/10 &start[]-position, const \OT1/cmr/bx/n/10 j-Vect or \OT1/cmr/m/n/10 &curr[]- [] [261 ] [262] [263] [264] Overfull \hbox (60.32071pt too wide) in paragraph at lines 300--300 []\OT1/cmtt/m/n/8 00153 printf(" start_ineq, end_ineq = %lf %lf\n", SegList.GetSeg(ixx).start, SegList.GetSeg(ixx).end );[] [] Overfull \hbox (13.57004pt too wide) in paragraph at lines 300--300 []\OT1/cmtt/m/n/8 00191 // if no violation at current qmin_dist, then Tem pSegment will be 0,0 -- break out of loop.[] [] Overfull \hbox (60.32071pt too wide) in paragraph at lines 300--300 []\OT1/cmtt/m/n/8 00202 printf(" start_ineq, end_ineq = %lf %lf\n", SegList.GetSeg(ixx).start, SegList.GetSeg(ixx).end );[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [265] Overfull \hbox (68.82083pt too wide) in paragraph at lines 386--386 []\OT1/cmtt/m/n/8 00317 printf(" initial x0, y0, z0 = %lf %lf %lf\n", st art_position[0], start_position[1], start_position[2]);[] [] Overfull \hbox (43.32047pt too wide) in paragraph at lines 386--386 []\OT1/cmtt/m/n/8 00318 printf(" initial x, y, z = %lf %lf %lf\n", curr_ position[0], curr_position[1], curr_position[2]);[] [] Overfull \hbox (30.57028pt too wide) in paragraph at lines 386--386 []\OT1/cmtt/m/n/8 00319 printf(" initial direction vector = %lf %lf %lf\ n", direction[0], direction[1], direction[2]);[] [] Overfull \hbox (5.06992pt too wide) in paragraph at lines 386--386 []\OT1/cmtt/m/n/8 00329 // double radius = LinearThreshold(sqrt(CM.stress(at om_index, curr_position)), LPertRadius);[] [] [266] Overfull \hbox (9.31998pt too wide) in paragraph at lines 386--386 []\OT1/cmtt/m/n/8 00342 cerr << "addLPERTSegments: pert stress = " << CM.s tress(atom_index, new_position) << endl;[] [] Overfull \hbox (94.3212pt too wide) in paragraph at lines 386--386 []\OT1/cmtt/m/n/8 00350 //radius = LinearThreshold(LPertRadius[2]-(1/(CM.stre ss(atom_index, curr_position)+LPertRadius[0])), LPertRadius);[] [] [267] Overfull \hbox (56.07065pt too wide) in paragraph at lines 475--475 []\OT1/cmtt/m/n/8 00250 // cerr << "Bonds for atom " << atom_index << ": " << CM.getMolecule().GetBonds(atom_index) << endl;[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [268] [269] [270]) [271] \openout2 = `class_gwRelaxAtom.aux'. (class_gwRelaxAtom.tex File: class_gwRelaxAtom_inherit_graph.eps Graphic file (type eps) File: class_gwRelaxAtom_coll_graph.eps Graphic file (type eps) [272 ] [273] Overfull \hbox (56.07065pt too wide) in paragraph at lines 343--343 []\OT1/cmtt/m/n/8 00031 cerr << "Value: \tgwRelexAtom::run() priority atom " << atom_index << "before ="<< getPriority() << endl;[] [] [274] Overfull \hbox (34.82034pt too wide) in paragraph at lines 343--343 []\OT1/cmtt/m/n/8 00084 printf(" x0, y0, z0 = %lf, %lf, %lf\n", start_posi tion[0], start_position[1], start_position[2]);[] [] Overfull \hbox (5.06992pt too wide) in paragraph at lines 343--343 []\OT1/cmtt/m/n/8 00092 cerr << "Working\tgwRelaxAtom::run() start iteratio n number " << iteration << endl << endl;[] [] Overfull \hbox (43.32047pt too wide) in paragraph at lines 343--343 []\OT1/cmtt/m/n/8 00093 cerr << "Value: \tgwRelaxAtom::run() step_position (start of iteration)= " << step_position <getMol ecule()(atom_index)[0], CM->getMolecule()(atom_index)[1],[] [] [277]) [278] \openout2 = `class_IdGen.aux'. (class_IdGen.tex File: class_IdGen_coll_graph.eps Graphic file (type eps) [279 ] [280] [281]) [282] \openout2 = `class_IntPriorityQueue.aux'. (class_IntPriorityQueue.tex [283 ] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294]) [295] \openout2 = `class_IntVec.aux'. (class_IntVec.tex [296 ] [297] Underfull \hbox (badness 10000) in paragraph at lines 198--198 []\OT1/cmr/m/n/10 Referenced by Atom::Add-Bond(), Constraint::add-Atom-Support( ), and Constraint::add- [] [298] Underfull \hbox (badness 10000) in paragraph at lines 272--272 []\OT1/cmr/m/n/10 Referenced by Con-straint::Input(), Constraint-Manager::add() , Con-straint::arity(), [] Underfull \hbox (badness 10000) in paragraph at lines 272--272 \OT1/cmr/m/n/10 Constraint::assert-Validity(), Constraint-Manager::get-Assoc-At oms(), and Constraint::notify- [] [299] [300] [301] [302] [303]) [304] \openout2 = `class_Iterator.aux'. (class_Iterator.tex File: class_Iterator_coll_graph.eps Graphic file (type eps) [305 ] [306]) [307] \openout2 = `class_ABitSet__Iterator.aux'. (class_ABitSet__Iterator.tex File: class_ABitSet__Iterator_coll_graph.eps Graphic file (type eps) [308 ] [309]) [310] \openout2 = `class_jdErr_Eval.aux'. (class_jdErr_Eval.tex File: class_jdErr_Eval_inherit_graph.eps Graphic file (type eps) File: class_jdErr_Eval_coll_graph.eps Graphic file (type eps) [311 ] [312] Overfull \hbox (5.06992pt too wide) in paragraph at lines 200--200 []\OT1/cmtt/m/n/8 00091 << "======================================== ==============================" << endl;[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [313]) [314] \openout2 = `class_jdIterator.aux'. (class_jdIterator.tex File: class_jdIterator_inherit_graph.eps Graphic file (type eps) File: class_jdIterator_coll_graph.eps Graphic file (type eps) [315 ] [316] Overfull \hbox (17.8201pt too wide) in paragraph at lines 154--154 []\OT1/cmtt/m/n/8 00070 StopFlag = Children[2]->run(); //editing this stil l -- performs evaluations and stop criteria[] [] ) [317] \openout2 = `class_jdOcc_Count.aux'. (class_jdOcc_Count.tex File: class_jdOcc_Count_inherit_graph.eps Graphic file (type eps) File: class_jdOcc_Count_coll_graph.eps Graphic file (type eps) [318 ] [319]) [320] \openout2 = `class_jdRand_Eval.aux'. (class_jdRand_Eval.tex File: class_jdRand_Eval_inherit_graph.eps Graphic file (type eps) File: class_jdRand_Eval_coll_graph.eps Graphic file (type eps) [321 ] [322] Overfull \hbox (5.06992pt too wide) in paragraph at lines 151--151 []\OT1/cmtt/m/n/8 00059 << "======================================== ==============================" << endl;[] [] Overfull \hbox (13.57004pt too wide) in paragraph at lines 151--151 []\OT1/cmtt/m/n/8 00066 << "====================================== ================================" << endl;[] [] Underfull \vbox (badness 1122) has occurred while \output is active [] [323]) [324] \openout2 = `class_jVector.aux'. (class_jVector.tex File: class_jVector_coll_graph.eps Graphic file (type eps) [325 ] [326] [327] [328] [329] [330] Underfull \hbox (badness 4967) in paragraph at lines 443--443 []\OT1/cmr/m/n/10 Referenced by Envelope-Constraint::Find-Model-Translation-To- COM(), JVAn-gle(), Envelope- [] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340]) [341] \openout2 = `class_KAdjMat.aux'. (class_KAdjMat.tex File: class_KAdjMat_coll_graph.eps Graphic file (type eps) [342 ] [343]) [344] \openout2 = `class_Matrix.aux'. (class_Matrix.tex [345 ] [346] [347] [348] Underfull \vbox (badness 10000) has occurred while \output is active [] [349] [350] [351] [352] [353] [354]) [355] \openout2 = `class_Molecule.aux'. (class_Molecule.tex File: class_Molecule_coll_graph.eps Graphic file (type eps) [356 ] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 10000) in paragraph at lines 503--503 []\OT1/cmr/m/n/10 Referenced by En-ve-lope::Build(), Constraint-Manager::Constr aint-Manager(), Constraint- [] Underfull \hbox (badness 10000) in paragraph at lines 503--503 \OT1/cmr/m/n/10 Manager::Random-Perturb(), Constraint-Manager::Turn-Atom-On(), Constraint-Manager::Turn- [] Underfull \hbox (badness 8170) in paragraph at lines 503--503 \OT1/cmr/m/n/10 Atoms-Off(), Envelope::Write-Density(), Constraint-Manager::cle ar-Constraints(), Constraint- [] Underfull \hbox (badness 10000) in paragraph at lines 503--503 \OT1/cmr/m/n/10 Manager::get-Assoc-Atoms(), Constraint-Manager::get-Stress-List (), Constraint-Manager::num- [] Underfull \hbox (badness 5711) in paragraph at lines 503--503 \OT1/cmr/m/n/10 Atoms(), Constraint-Manager::reset-Moved(), Constraint-Manager: :set-Molecule(), Constraint- [] [364] [365] [366] [367] [368] [369] [370] [371] [372]) [373] \openout2 = `class_neighbor_iterator.aux'. (class_neighbor_iterator.tex File: class_neighbor_iterator_inherit_graph.eps Graphic file (type eps) File: class_neighbor_iterator_coll_graph.eps Graphic file (type eps) [374 ] [375]) [376] \openout2 = `class_path_iterator.aux'. (class_path_iterator.tex File: class_path_iterator_coll_graph.eps Graphic file (type eps) [377 ] [378] [379] [380] [381] [382] [383]) [384] \openout2 = `class_PositionConstraint.aux'. (class_PositionConstraint.tex File: class_PositionConstraint_inherit_graph.eps Graphic file (type eps) File: class_PositionConstraint_coll_graph.eps Graphic file (type eps) [385 ] [386] [387] [388] [389]) [390] \openout2 = `class_Process.aux'. (class_Process.tex File: class_Process_inherit_graph.eps Graphic file (type eps) File: class_Process_coll_graph.eps Graphic file (type eps) [391 ] [392] [393] [394] [395] [396] [397] [398]) [399] \openout2 = `class_Queue.aux'. (class_Queue.tex File: class_Queue_inherit_graph.eps Graphic file (type eps) File: class_Queue_coll_graph.eps Graphic file (type eps) [400 ] [401]) [402] \openout2 = `class_RanBaseClass.aux'. (class_RanBaseClass.tex File: class_RanBaseClass_inherit_graph.eps Graphic file (type eps) [403 ] [404]) [405] \openout2 = `class_RanChar.aux'. (class_RanChar.tex File: class_RanChar_inherit_graph.eps Graphic file (type eps) File: class_RanChar_coll_graph.eps Graphic file (type eps) [406 ]) [407] \openout2 = `class_RanDbl.aux'. (class_RanDbl.tex File: class_RanDbl_inherit_graph.eps Graphic file (type eps) File: class_RanDbl_coll_graph.eps Graphic file (type eps) [408 ]) [409] \openout2 = `class_RanInt.aux'. (class_RanInt.tex File: class_RanInt_inherit_graph.eps Graphic file (type eps) File: class_RanInt_coll_graph.eps Graphic file (type eps) [410 ]) [411] \openout2 = `class_RanLetter.aux'. (class_RanLetter.tex File: class_RanLetter_inherit_graph.eps Graphic file (type eps) File: class_RanLetter_coll_graph.eps Graphic file (type eps) [412 ]) [413] \openout2 = `class_RanWord.aux'. (class_RanWord.tex File: class_RanWord_inherit_graph.eps Graphic file (type eps) File: class_RanWord_coll_graph.eps Graphic file (type eps) [414 ]) [415] \openout2 = `class_RefRep.aux'. (class_RefRep.tex File: class_RefRep_inherit_graph.eps Graphic file (type eps) [416 ] Underfull \hbox (badness 10000) in paragraph at lines 73--73 []\OT1/cmr/m/n/10 Referenced by Const-Iterator::Copy(), It-er-a-tor::Copy(), DL -List::operator=(), AM-a- [] Underfull \hbox (badness 5787) in paragraph at lines 89--89 []\OT1/cmr/m/n/10 Referenced by AM-a-trix::AMatrix(), Const-Iterator::Const-Ite rator(), Const-Iterator::Copy(), [] Underfull \hbox (badness 7168) in paragraph at lines 89--89 \OT1/cmr/m/n/10 It-er-a-tor::Copy(), DL-List::DLList(), It-er-a-tor::Iterator() , DL-List::operator=(), and AM-a- [] ) [417] \openout2 = `class_RelaxSubset.aux'. (class_RelaxSubset.tex File: class_RelaxSubset_inherit_graph.eps Graphic file (type eps) File: class_RelaxSubset_coll_graph.eps Graphic file (type eps) LaTeX Font Info: Font shape `OMS/cmr/m/it' in size <9> not available (Font) Font shape `OMS/cmsy/m/n' tried instead on input line 29. [418 ] [419] Underfull \vbox (badness 3942) has occurred while \output is active [] [420]) [421] \openout2 = `class_Residue.aux'. (class_Residue.tex File: class_Residue_coll_graph.eps Graphic file (type eps) [422 ] Overfull \hbox (30.57028pt too wide) in paragraph at lines 155--155 []\OT1/cmtt/m/n/8 00013 { [] [423] Overfull \hbox (13.57004pt too wide) in paragraph at lines 170--170 []\OT1/cmtt/m/n/8 00006 // cerr << "bonding " << Mol[atom_id1].Label() << " TO " << Mol[atom_id2].Label() < File: class_SatisfyMolecule_coll_graph.eps Graphic file (type eps) [438 ] [439]) [440] \openout2 = `class_sdEdge.aux'. (class_sdEdge.tex File: class_sdEdge_coll_graph.eps Graphic file (type eps) [441 ]) [442] \openout2 = `class_sdGraph.aux'. (class_sdGraph.tex File: class_sdGraph_coll_graph.eps Graphic file (type eps) [443 ] [444] [445] [446] Underfull \vbox (badness 10000) has occurred while \output is active [] [447] Underfull \vbox (badness 10000) has occurred while \output is active [] [448] [449] [450] [451] Underfull \hbox (badness 10000) in paragraph at lines 655--655 []\OT1/cmr/m/n/10 Referenced by Constraint-Manager::get-Assoc-Atoms(), Constrai nt-Manager::get-Constraint(), [] [452] [453] [454] [455] [456] [457] [458] [459] [460] Underfull \vbox (badness 10000) has occurred while \output is active [] [461] Underfull \vbox (badness 10000) has occurred while \output is active [] [462] [463] Underfull \vbox (badness 10000) has occurred while \output is active [] [464] [465] [466] [467] [468] [469]) [470] \openout2 = `class_sdVertex.aux'. (class_sdVertex.tex File: class_sdVertex_coll_graph.eps Graphic file (type eps) [471 ] [472] [473] [474] [475] [476] [477] [478]) [479] \openout2 = `class_Segment.aux'. (class_Segment.tex [480 ] [481]) [482] \openout2 = `class_Segments.aux'. (class_Segments.tex File: class_Segments_coll_graph.eps Graphic file (type eps) [483 ] [484] [485] Overfull \hbox (0.81985pt too wide) in paragraph at lines 260--260 []\OT1/cmtt/m/n/8 00162 cerr << "walking up through segment: ("<< testseg <<") ;?test overlap "< File: class_Stack_coll_graph.eps Graphic file (type eps) [488 ]) [489] \openout2 = `class_StopEval.aux'. (class_StopEval.tex File: class_StopEval_inherit_graph.eps Graphic file (type eps) File: class_StopEval_coll_graph.eps Graphic file (type eps) [490 ] [491] [492] Overfull \hbox (13.57004pt too wide) in paragraph at lines 227--227 []\OT1/cmtt/m/n/8 00104 << "----- ------- ------- ------- ---- ---------- ----- ----------- "[] [] [493] Overfull \hbox (0.81985pt too wide) in paragraph at lines 501--501 []\OT1/cmtt/m/n/8 00128 // // cerr << endl <<", " << gwNumerics::get_NumLP() << ", " << gwNumerics::get_NumNotLP();[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [494] Overfull \hbox (5.06992pt too wide) in paragraph at lines 501--501 []\OT1/cmtt/m/n/8 00188 // int listlength = TotalStressList.Number(); //Mu st check this, may not eval every cycle.[] [] Overfull \hbox (22.07016pt too wide) in paragraph at lines 501--501 []\OT1/cmtt/m/n/8 00203 // if (MinLookBackStress > tempY) MinLookBackStre ss = tempY; // set init min/max over list[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [495] Overfull \hbox (9.31998pt too wide) in paragraph at lines 501--501 []\OT1/cmtt/m/n/8 00247 // SumXX = SumXX + ((NumCalls)*(NumCalls) - OldX*Ol dX); // actually NumCalls-OldX=LookBack-1[] [] Overfull \hbox (94.3212pt too wide) in paragraph at lines 501--501 []\OT1/cmtt/m/n/8 00256 // Variance += (((LookBack*SumYY)-(SumY*SumY))-((Lo okBack*OldSumYY)-(OldSumY*OldSumY)))/(LookBack*(LookBack-1));[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [496] Underfull \vbox (badness 10000) has occurred while \output is active [] [497] [498] [499] [500]) [501] \openout2 = `class_UnitWeight.aux'. (class_UnitWeight.tex [502 ] [503]) [504] \openout2 = `class_z.aux'. (class_z.tex [505 ]) [506] Chapter 5. (abbrev_h.tex File: abbrev_h_dep_incl.eps Graphic file (type eps) Underfull \vbox (badness 2865) has occurred while \output is active [] [507 ]) [508] \openout2 = `abitset_C.aux'. (abitset_C.tex File: abitset_C_incl.eps Graphic file (type eps) [509 ] [510] LaTeX Font Info: Font shape `OMS/cmr/bx/n' in size <10> not available (Font) Font shape `OMS/cmsy/b/n' tried instead on input line 138. ) [511] \openout2 = `abitset_h.aux'. (abitset_h.tex File: abitset_h_incl.eps Graphic file (type eps) File: abitset_h_dep_incl.eps Graphic file (type eps) ) [512 ] \openout2 = `ajiobin_h.aux'. (ajiobin_h.tex File: ajiobin_h_incl.eps Graphic file (type eps) File: ajiobin_h_dep_incl.eps Graphic file (type eps) [513 ] [514] [515] [516] [517] [518] [519] [520] [521] [522]) [523] \openout2 = `amatrix_h.aux'. (amatrix_h.tex File: amatrix_h_incl.eps Graphic file (type eps) ) [524 ] \openout2 = `amatrix_inc.aux'. (amatrix_inc.tex File: amatrix_inc_dep_incl.eps Graphic file (type eps) ) [525 ] \openout2 = `atom_h.aux'. (atom_h.tex File: atom_h_incl.eps Graphic file (type eps) File: atom_h_dep_incl.eps Graphic file (type eps) [526 ]) [527] \openout2 = `atom_buildup_C.aux'. (atom_buildup_C.tex File: atom_buildup_C_incl.eps Graphic file (type eps) ) [528 ] \openout2 = `atom_buildup_h.aux'. (atom_buildup_h.tex File: atom_buildup_h_incl.eps Graphic file (type eps) File: atom_buildup_h_dep_incl.eps Graphic file (type eps) ) [529 ] \openout2 = `atom_constraint_C.aux'. (atom_constraint_C.tex File: atom_constraint_C_incl.eps Graphic file (type eps) ) [530 ] \openout2 = `atom_constraint_h.aux'. (atom_constraint_h.tex File: atom_constraint_h_incl.eps Graphic file (type eps) File: atom_constraint_h_dep_incl.eps Graphic file (type eps) ) [531 ] \openout2 = `atom_registry_C.aux'. (atom_registry_C.tex) [532 ] \openout2 = `atom_registry_h.aux'. (atom_registry_h.tex File: atom_registry_h_incl.eps Graphic file (type eps) File: atom_registry_h_dep_incl.eps Graphic file (type eps) [533 ]) [534] \openout2 = `bin_envelope_constraint_C.aux'. (bin_envelope_constraint_C.tex File: bin_envelope_constraint_C_incl.eps Graphic file (type eps) ) [535 ] \openout2 = `bin_envelope_constraint_h.aux'. (bin_envelope_constraint_h.tex File: bin_envelope_constraint_h_incl.eps Graphic file (type eps) File: bin_envelope_constraint_h_dep_incl.eps Graphic file (type eps) ) [536 ] \openout2 = `bits_h.aux'. (bits_h.tex File: bits_h_incl.eps Graphic file (type eps) File: bits_h_dep_incl.eps Graphic file (type eps) [537 ]) [538] \openout2 = `compoper_h.aux'. (compoper_h.tex File: compoper_h_dep_incl.eps Graphic file (type eps) [539 ]) [540] \openout2 = `constraint_C.aux'. (constraint_C.tex File: constraint_C_incl.eps Graphic file (type eps) ) [541 ] \openout2 = `constraint_h.aux'. (constraint_h.tex File: constraint_h_incl.eps Graphic file (type eps) File: constraint_h_dep_incl.eps Graphic file (type eps) [542 ]) [543] \openout2 = `constraint_manager_C.aux'. (constraint_manager_C.tex File: constraint_manager_C_incl.eps Graphic file (type eps) ) [544 ] \openout2 = `constraint_manager_h.aux'. (constraint_manager_h.tex File: constraint_manager_h_incl.eps Graphic file (type eps) File: constraint_manager_h_dep_incl.eps Graphic file (type eps) Underfull \vbox (badness 10000) has occurred while \output is active [] [545 ]) [546] \openout2 = `constraint_registry_C.aux'. (constraint_registry_C.tex File: constraint_registry_C_incl.eps Graphic file (type eps) ) [547 ] \openout2 = `constraint_registry_h.aux'. (constraint_registry_h.tex File: constraint_registry_h_incl.eps Graphic file (type eps) File: constraint_registry_h_dep_incl.eps Graphic file (type eps) ) [548 ] \openout2 = `cycle_all_C.aux'. (cycle_all_C.tex File: cycle_all_C_incl.eps Graphic file (type eps) ) [549 ] \openout2 = `cycle_all_h.aux'. (cycle_all_h.tex File: cycle_all_h_incl.eps Graphic file (type eps) File: cycle_all_h_dep_incl.eps Graphic file (type eps) ) [550 ] \openout2 = `ddgraph_h.aux'. (ddgraph_h.tex File: ddgraph_h_incl.eps Graphic file (type eps) File: ddgraph_h_dep_incl.eps Graphic file (type eps) Underfull \vbox (badness 1436) has occurred while \output is active [] [551 ] Underfull \hbox (badness 10000) in paragraph at lines 74--74 [] [552] [553]) [554] \openout2 = `ddgraph_inc.aux'. (ddgraph_inc.tex File: ddgraph_inc_dep_incl.eps Graphic file (type eps) [555 ]) [556] \openout2 = `ddvertex_h.aux'. (ddvertex_h.tex File: ddvertex_h_incl.eps Graphic file (type eps) File: ddvertex_h_dep_incl.eps Graphic file (type eps) ) [557 ] \openout2 = `ddvertex_inc.aux'. (ddvertex_inc.tex File: ddvertex_inc_dep_incl.eps Graphic file (type eps) ) [558 ] \openout2 = `dens-trans_C.aux'. (dens-trans_C.tex File: dens-trans_C_incl.eps Graphic file (type eps) [559 ] Overfull \hbox (26.32022pt too wide) in paragraph at lines 113--113 []\OT1/cmtt/m/n/8 00081 cerr << "reading error!\n read "<< read << " entries, expected "<< xdim*ydim*zdim << endl;[] [] ) [560] \openout2 = `dist_C.aux'. (dist_C.tex File: dist_C_incl.eps Graphic file (type eps) ) [561 ] \openout2 = `distance_constraint_C.aux'. (distance_constraint_C.tex File: distance_constraint_C_incl.eps Graphic file (type eps) ) [562 ] \openout2 = `distance_constraint_h.aux'. (distance_constraint_h.tex File: distance_constraint_h_incl.eps Graphic file (type eps) File: distance_constraint_h_dep_incl.eps Graphic file (type eps) ) [563 ] \openout2 = `dllist_h.aux'. (dllist_h.tex File: dllist_h_incl.eps Graphic file (type eps) File: dllist_h_dep_incl.eps Graphic file (type eps) ) [564 ] \openout2 = `dllist_inc.aux'. (dllist_inc.tex File: dllist_inc_dep_incl.eps Graphic file (type eps) [565 ]) [566] \openout2 = `dlliter_inc.aux'. (dlliter_inc.tex File: dlliter_inc_dep_incl.eps Graphic file (type eps) ) [567 ] \openout2 = `dsiter_inc.aux'. (dsiter_inc.tex File: dsiter_inc_dep_incl.eps Graphic file (type eps) ) [568 ] \openout2 = `dynstring_C.aux'. (dynstring_C.tex File: dynstring_C_incl.eps Graphic file (type eps) [569 ]) [570] \openout2 = `dynstring_h.aux'. (dynstring_h.tex File: dynstring_h_incl.eps Graphic file (type eps) File: dynstring_h_dep_incl.eps Graphic file (type eps) Underfull \vbox (badness 10000) has occurred while \output is active [] [571 ]) [572] \openout2 = `env_diff_C.aux'. (env_diff_C.tex File: env_diff_C_incl.eps Graphic file (type eps) ) [573 ] \openout2 = `envelope_C.aux'. (envelope_C.tex File: envelope_C_incl.eps Graphic file (type eps) ) [574 ] \openout2 = `envelope_h.aux'. (envelope_h.tex File: envelope_h_incl.eps Graphic file (type eps) File: envelope_h_dep_incl.eps Graphic file (type eps) Underfull \vbox (badness 10000) has occurred while \output is active [] [575 ]) [576] \openout2 = `envelope_constraint_C.aux'. (envelope_constraint_C.tex File: envelope_constraint_C_incl.eps Graphic file (type eps) ) [577 ] \openout2 = `envelope_constraint_h.aux'. (envelope_constraint_h.tex File: envelope_constraint_h_incl.eps Graphic file (type eps) File: envelope_constraint_h_dep_incl.eps Graphic file (type eps) ) [578 ] \openout2 = `err_eval_C.aux'. (err_eval_C.tex File: err_eval_C_incl.eps Graphic file (type eps) [579 ] Underfull \vbox (badness 10000) has occurred while \output is active [] [580] Underfull \vbox (badness 10000) has occurred while \output is active [] [581] Underfull \vbox (badness 10000) has occurred while \output is active [] [582] Overfull \hbox (34.82034pt too wide) in paragraph at lines 317--317 []\OT1/cmtt/m/n/8 00244 cerr << "Error reading initial positions fr om " << positionFile << ". Check the file.\n";[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [583]) [584] \openout2 = `error_handler_h.aux'. (error_handler_h.tex File: error_handler_h_incl.eps Graphic file (type eps) File: error_handler_h_dep_incl.eps Graphic file (type eps) Underfull \hbox (badness 3291) in paragraph at lines 48--50 []\OT1/cmr/m/n/10 Referenced by Anim-Frame::Anim-Frame(), Atom-Buildup::Atom-Bu ildup(), En-ve-lope::Blur(), [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Envelope::Calc-Gradient(), Envelope-Constraint::Compare(), En-v e-lope::Compare(), Bin- [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Envelope-Constraint::Compare(), Envelope-Constraint::Pre-Setup( ), Envelope::Read- [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Avs-Txt(), Molecule::Reallocate(), Relax-Subset::Relax-Subset() , Anim-Frame::Set[]- [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Output[]-Stream(), Stop-Eval::Stop-Eval(), Constraint-Manager:: Turn-Atom-On(), En-ve- [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 lope::Upsize(), Constraint-Manager::add(), Process::assert-Orde r(), Constraint::assert- [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Validity(), Position-Constraint::compute-Stress(), Envelope-Con straint::compute-Stress(), [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Distance-Constraint::compute-Stress(), Bin-Envelope-Constraint: :compute-Stress(), Atom- [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Constraint::compute-Stress(), Position-Constraint::d-Stress(), Distance-Constraint::d-Stress(), [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Constraint(), Constraint-Registry::get-Int-Type(), Constraint-M anager::get-Parents(), Ma- [] Underfull \hbox (badness 2564) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Atom-Constraint::notify-Remove(), Atom-Constraint::notify-Valid (), Ma-trix::operator $\OMS/cmsy/m/n/10 ^^C$\OT1/cmr/m/n/10 (), Ma- [] Underfull \hbox (badness 10000) in paragraph at lines 48--50 \OT1/cmr/m/n/10 Registry::read-Constraints(), Molecule::read-Xmol(), Constraint -Manager::register-Envelope(), [] [585 ] Underfull \hbox (badness 10000) in paragraph at lines 61--63 []\OT1/cmr/m/n/10 Referenced by Envelope-Constraint::Align-Modelto-COM(), En-ve -lope::Center(), [] ) [586] \openout2 = `globals_C.aux'. (globals_C.tex File: globals_C_incl.eps Graphic file (type eps) ) [587 ] \openout2 = `globals_h.aux'. (globals_h.tex File: globals_h_incl.eps Graphic file (type eps) File: globals_h_dep_incl.eps Graphic file (type eps) [588 ]) [589] \openout2 = `grape_C.aux'. (grape_C.tex File: grape_C_incl.eps Graphic file (type eps) [590 ] Underfull \vbox (badness 10000) has occurred while \output is active [] [591] Underfull \vbox (badness 10000) has occurred while \output is active [] [592] Underfull \vbox (badness 10000) has occurred while \output is active [] [593] Underfull \vbox (badness 10000) has occurred while \output is active [] [594] Overfull \hbox (43.32047pt too wide) in paragraph at lines 461--461 []\OT1/cmtt/m/n/8 00353 cerr << "Error reading initial positions from " << positionFile << ". Check the file.\n";[] [] Underfull \vbox (badness 10000) has occurred while \output is active [] [595] Underfull \vbox (badness 10000) has occurred while \output is active [] [596] [597]) [598] \openout2 = `graph_weights_h.aux'. (graph_weights_h.tex File: graph_weights_h_incl.eps Graphic file (type eps) File: graph_weights_h_dep_incl.eps Graphic file (type eps) ) [599 ] \openout2 = `grid_C.aux'. (grid_C.tex File: grid_C_incl.eps Graphic file (type eps) ) [600 ] \openout2 = `grid_h.aux'. (grid_h.tex File: grid_h_incl.eps Graphic file (type eps) File: grid_h_dep_incl.eps Graphic file (type eps) Underfull \hbox (badness 2903) in paragraph at lines 34--36 []\OT1/cmr/m/n/10 typedef hash[]-multimap$\OML/cmm/m/it/10 <$\OT1/cmr/m/n/10 c onst \OT1/cmr/bx/n/10 Grid-Number\OT1/cmr/m/n/10 , int, hash$\OML/cmm/m/it/10 < $\OT1/cmr/m/n/10 long$\OML/cmm/m/it/10 >$\OT1/cmr/m/n/10 , equal[]-to$\OML/cmm/ m/it/10 <$\OT1/cmr/m/n/10 long$\OML/cmm/m/it/10 >$ $>$ [] [601 ]) [602] \openout2 = `gw_numerics_C.aux'. (gw_numerics_C.tex File: gw_numerics_C_incl.eps Graphic file (type eps) ) [603 ] \openout2 = `gw_numerics_h.aux'. (gw_numerics_h.tex File: gw_numerics_h_incl.eps Graphic file (type eps) File: gw_numerics_h_dep_incl.eps Graphic file (type eps) ) [604 ] \openout2 = `gw_relax_atom_C.aux'. (gw_relax_atom_C.tex File: gw_relax_atom_C_incl.eps Graphic file (type eps) ) [605 ] \openout2 = `gw_relax_atom_h.aux'. (gw_relax_atom_h.tex File: gw_relax_atom_h_incl.eps Graphic file (type eps) File: gw_relax_atom_h_dep_incl.eps Graphic file (type eps) ) [606 ] \openout2 = `idgen_h.aux'. (idgen_h.tex File: idgen_h_incl.eps Graphic file (type eps) File: idgen_h_dep_incl.eps Graphic file (type eps) ) [607 ] \openout2 = `intvec_C.aux'. (intvec_C.tex File: intvec_C_incl.eps Graphic file (type eps) ) [608 ] \openout2 = `intvec_h.aux'. (intvec_h.tex File: intvec_h_incl.eps Graphic file (type eps) File: intvec_h_dep_incl.eps Graphic file (type eps) ) [609 ] \openout2 = `intvec_inc.aux'. (intvec_inc.tex File: intvec_inc_dep_incl.eps Graphic file (type eps) [610 ] [611]) [612] \openout2 = `ipqueue_h.aux'. (ipqueue_h.tex File: ipqueue_h_incl.eps Graphic file (type eps) File: ipqueue_h_dep_incl.eps Graphic file (type eps) ) [613 ] \openout2 = `ipqueue_inc.aux'. (ipqueue_inc.tex File: ipqueue_inc_dep_incl.eps Graphic file (type eps) ) [614 ] \openout2 = `jd_anim_frame_C.aux'. (jd_anim_frame_C.tex File: jd_anim_frame_C_incl.eps Graphic file (type eps) ) [615 ] \openout2 = `jd_anim_frame_h.aux'. (jd_anim_frame_h.tex File: jd_anim_frame_h_incl.eps Graphic file (type eps) File: jd_anim_frame_h_dep_incl.eps Graphic file (type eps) ) [616 ] \openout2 = `jd_err_eval_C.aux'. (jd_err_eval_C.tex File: jd_err_eval_C_incl.eps Graphic file (type eps) ) [617 ] \openout2 = `jd_err_eval_h.aux'. (jd_err_eval_h.tex File: jd_err_eval_h_incl.eps Graphic file (type eps) File: jd_err_eval_h_dep_incl.eps Graphic file (type eps) ) [618 ] \openout2 = `jd_iterator_C.aux'. (jd_iterator_C.tex File: jd_iterator_C_incl.eps Graphic file (type eps) ) [619 ] \openout2 = `jd_iterator_h.aux'. (jd_iterator_h.tex File: jd_iterator_h_incl.eps Graphic file (type eps) File: jd_iterator_h_dep_incl.eps Graphic file (type eps) ) [620 ] \openout2 = `jd_occ_count_C.aux'. (jd_occ_count_C.tex File: jd_occ_count_C_incl.eps Graphic file (type eps) ) [621 ] \openout2 = `jd_occ_count_h.aux'. (jd_occ_count_h.tex File: jd_occ_count_h_incl.eps Graphic file (type eps) File: jd_occ_count_h_dep_incl.eps Graphic file (type eps) ) [622 ] \openout2 = `jd_rand_eval_C.aux'. (jd_rand_eval_C.tex File: jd_rand_eval_C_incl.eps Graphic file (type eps) ) [623 ] \openout2 = `jd_rand_eval_h.aux'. (jd_rand_eval_h.tex File: jd_rand_eval_h_incl.eps Graphic file (type eps) File: jd_rand_eval_h_dep_incl.eps Graphic file (type eps) ) [624 ] \openout2 = `jd_relax_subset_C.aux'. (jd_relax_subset_C.tex File: jd_relax_subset_C_incl.eps Graphic file (type eps) ) [625 ] \openout2 = `jd_relax_subset_h.aux'. (jd_relax_subset_h.tex File: jd_relax_subset_h_incl.eps Graphic file (type eps) File: jd_relax_subset_h_dep_incl.eps Graphic file (type eps) ) [626 ] \openout2 = `jd_stop_eval_C.aux'. (jd_stop_eval_C.tex File: jd_stop_eval_C_incl.eps Graphic file (type eps) ) [627 ] \openout2 = `jd_stop_eval_h.aux'. (jd_stop_eval_h.tex File: jd_stop_eval_h_incl.eps Graphic file (type eps) File: jd_stop_eval_h_dep_incl.eps Graphic file (type eps) ) [628 ] \openout2 = `jsmisc_h.aux'. (jsmisc_h.tex File: jsmisc_h_incl.eps Graphic file (type eps) File: jsmisc_h_dep_incl.eps Graphic file (type eps) [629 ]) [630] \openout2 = `jvector_C.aux'. (jvector_C.tex File: jvector_C_incl.eps Graphic file (type eps) [631 ] [632] Underfull \hbox (badness 10000) in paragraph at lines 153--153 []\OT1/cmr/m/n/10 Referenced by gw-Numerics::add-VDWSegments(), Distance-Constr aint::compute-Abs-Res(), [] Underfull \hbox (badness 10000) in paragraph at lines 153--153 \OT1/cmr/m/n/10 Distance-Constraint::compute-Stress(), Position-Constraint::d-S tress(), Distance-Constraint::d- [] [633]) [634] \openout2 = `jvector_h.aux'. (jvector_h.tex File: jvector_h_incl.eps Graphic file (type eps) File: jvector_h_dep_incl.eps Graphic file (type eps) [635 ]) [636] [637] \openout2 = `kadjmat_h.aux'. (kadjmat_h.tex File: kadjmat_h_incl.eps Graphic file (type eps) File: kadjmat_h_dep_incl.eps Graphic file (type eps) ) [638 ] \openout2 = `LeakTracer_Makefile.aux'. (LeakTracer_Makefile.tex) [639 ] \openout2 = `lib_Makefile.aux'. (lib_Makefile.tex) [640 ] \openout2 = `Makefile.aux'. (Makefile.tex) [641 ] \openout2 = `src_aux_Makefile.aux'. (src_aux_Makefile.tex) [642 ] \openout2 = `src_Makefile.aux'. (src_Makefile.tex) [643 ] \openout2 = `matrix_C.aux'. (matrix_C.tex File: matrix_C_incl.eps Graphic file (type eps) ) [644 ] \openout2 = `matrix_h.aux'. (matrix_h.tex File: matrix_h_incl.eps Graphic file (type eps) File: matrix_h_dep_incl.eps Graphic file (type eps) [645 ]) [646] \openout2 = `molecule_C.aux'. (molecule_C.tex File: molecule_C_incl.eps Graphic file (type eps) ) [647 ] \openout2 = `molecule_h.aux'. (molecule_h.tex File: molecule_h_incl.eps Graphic file (type eps) File: molecule_h_dep_incl.eps Graphic file (type eps) Underfull \vbox (badness 10000) has occurred while \output is active [] [648 ]) [649] \openout2 = `molio_C.aux'. (molio_C.tex File: molio_C_incl.eps Graphic file (type eps) ) [650 ] \openout2 = `ocount_C.aux'. (ocount_C.tex File: ocount_C_incl.eps Graphic file (type eps) [651 ] Underfull \vbox (badness 10000) has occurred while \output is active [] [652] Underfull \vbox (badness 10000) has occurred while \output is active [] [653]) [654] \openout2 = `position_constraint_C.aux'. (position_constraint_C.tex File: position_constraint_C_incl.eps Graphic file (type eps) ) [655 ] \openout2 = `position_constraint_h.aux'. (position_constraint_h.tex File: position_constraint_h_incl.eps Graphic file (type eps) File: position_constraint_h_dep_incl.eps Graphic file (type eps) ) [656 ] \openout2 = `process_C.aux'. (process_C.tex File: process_C_incl.eps Graphic file (type eps) ) [657 ] \openout2 = `process_h.aux'. (process_h.tex File: process_h_incl.eps Graphic file (type eps) File: process_h_dep_incl.eps Graphic file (type eps) ) [658 ] \openout2 = `queue_h.aux'. (queue_h.tex File: queue_h_incl.eps Graphic file (type eps) File: queue_h_dep_incl.eps Graphic file (type eps) ) [659 ] \openout2 = `rand_eval_C.aux'. (rand_eval_C.tex File: rand_eval_C_incl.eps Graphic file (type eps) [660 ] Underfull \vbox (badness 10000) has occurred while \output is active [] [661] Underfull \vbox (badness 10000) has occurred while \output is active [] [662] Underfull \vbox (badness 10000) has occurred while \output is active [] [663]) [664] \openout2 = `randomgenerator_C.aux'. (randomgenerator_C.tex File: randomgenerator_C_incl.eps Graphic file (type eps) ) [665 ] \openout2 = `randomgenerator_h.aux'. 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