Changes in / [51a5c8:f0f1cc]


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  • configure.ac

    r51a5c8 rf0f1cc  
    3333AX_BOOST_THREAD
    3434#AX_BOOST_SERIALIZATION
    35 
    36 #QT4 libraries
    37 gw_CHECK_QT4
    38 AX_CHECK_GLU
    39 AC_MSG_NOTICE(["GLU_CFLAGS: $GLU_CFLAGS, GLU_CXXFLAGS: $GLU_CXXFLAGS, GLU_LDFLAGS: $GLU_LDFLAGS, GLU_LIBS: $GLU_LIBS"])
    40 
    4135
    4236# Checks for header files.

  • doc/class structure.uxf

    r51a5c8 rf0f1cc  
    2121
    2222
    23 // This text will be stored with each diagram;  use it for notes.</help_text><zoom_level>7</zoom_level><element><type>com.umlet.element.base.Class</type><coordinates><x>1855</x><y>210</y><w>147</w><h>70</h></coordinates><panel_attributes>AtomInfo
     23// This text will be stored with each diagram;  use it for notes.</help_text><zoom_level>7</zoom_level><element><type>com.umlet.element.base.Class</type><coordinates><x>1855</x><y>294</y><w>147</w><h>70</h></coordinates><panel_attributes>AtomInfo
    2424--
    2525-x,v,F: Vector
    … …  
    2828#AtomInfo();
    2929#~AtomInfo();
    30 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1645</x><y>231</y><w>223</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>210;21;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1274</x><y>63</y><w>392</w><h>259</h></coordinates><panel_attributes>Element
     30</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1645</x><y>315</y><w>223</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>210;21;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1274</x><y>147</y><w>392</w><h>259</h></coordinates><panel_attributes>Element
    3131--
    3232mass: double
    … …  
    4949#~element();
    5050#Output(ofstream * const out) const: bool
    51 #Checkout(ofstream * const out, const int No, const int NoOfAtoms) const: bool</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1960</x><y>448</y><w>280</w><h>161</h></coordinates><panel_attributes>BondedParticle
     51#Checkout(ofstream * const out, const int No, const int NoOfAtoms) const: bool</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1960</x><y>532</y><w>280</w><h>161</h></coordinates><panel_attributes>BondedParticle
    5252--
    5353--
    … …  
    6363#OutputBondOfAtom() const
    6464#OutputAdjacency(ofstream *AdjacencyFile) const
    65 #OutputOrder(ofstream *file) const</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2184</x><y>259</y><w>258</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>245;21;245;154;21;154;21;189</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1925</x><y>259</y><w>293</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-
    66 </panel_attributes><additional_attributes>21;21;21;154;280;154;280;189</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2184</x><y>259</y><w>34</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;189</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2359</x><y>210</y><w>147</w><h>70</h></coordinates><panel_attributes>BondedParticleInfo
     65#OutputOrder(ofstream *file) const</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2184</x><y>343</y><w>258</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>245;21;245;154;21;154;21;189</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1925</x><y>343</y><w>293</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-
     66</panel_attributes><additional_attributes>21;21;21;154;280;154;280;189</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2184</x><y>343</y><w>34</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;189</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2359</x><y>294</y><w>147</w><h>70</h></coordinates><panel_attributes>BondedParticleInfo
    6767--
    6868AdaptiveOrder: unsigned char
    … …  
    7171#BondedParticleInfo()
    7272#~BondedParticleInfo()
    73 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2079</x><y>196</y><w>217</w><h>84</h></coordinates><panel_attributes>ParticleInfo
     73</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2079</x><y>280</y><w>217</w><h>84</h></coordinates><panel_attributes>ParticleInfo
    7474--
    7575nr: int
    … …  
    7979#~ParticleInfo()
    8080#ostream &amp; operator &lt;&lt; (ostream &amp;ost) const
    81 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2485</x><y>231</y><w>174</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;161;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2646</x><y>161</y><w>147</w><h>133</h></coordinates><panel_attributes>BondList
     81</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2485</x><y>315</y><w>174</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;161;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2646</x><y>245</y><w>147</w><h>133</h></coordinates><panel_attributes>BondList
    8282{Some Properties}
    8383--
    … …  
    9090Responsibilities
    9191-- Resp1
    92 *-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1372</x><y>343</y><w>147</w><h>105</h></coordinates><panel_attributes>GraphNodeInfo
     92*-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1372</x><y>427</y><w>147</w><h>105</h></coordinates><panel_attributes>GraphNodeInfo
    9393--
    9494--
    … …  
    102102#GraphNodeInfo()
    103103#~GraphNodeInfo()
    104 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1484</x><y>525</y><w>126</w><h>70</h></coordinates><panel_attributes>GraphNode
     104</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1484</x><y>609</y><w>126</w><h>70</h></coordinates><panel_attributes>GraphNode
    105105--
    106106--
    … …  
    109109#OutputGraphInfo() const
    110110#OutputComponentNumber() const
    111 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1484</x><y>259</y><w>748</w><h>279</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>735;21;735;70;217;70;217;210;21;210;21;266</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1484</x><y>427</y><w>34</w><h>111</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;98</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1288</x><y>672</y><w>588</w><h>245</h></coordinates><panel_attributes>Atom
     111</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1484</x><y>343</y><w>748</w><h>279</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>735;21;735;70;217;70;217;210;21;210;21;266</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1484</x><y>511</y><w>34</w><h>111</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;98</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1288</x><y>756</y><w>588</w><h>245</h></coordinates><panel_attributes>Atom
    112112--
    113113sort: int*
    … …  
    129129#DistanceToVector(const Vector &amp;origin) const: double
    130130#DistanceSquaredToVector(const Vector &amp;origin) const: double
    131 #IsInParallelepiped(const Vector offset, const double *parallelepiped) const: bool</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1379</x><y>427</y><w>83</w><h>258</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;182;70;182;70;245</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2226</x><y>665</y><w>504</w><h>210</h></coordinates><panel_attributes>TrajectoryParticle
     131#IsInParallelepiped(const Vector offset, const double *parallelepiped) const: bool</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1379</x><y>511</y><w>83</w><h>258</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;182;70;182;70;245</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2226</x><y>749</y><w>504</w><h>210</h></coordinates><panel_attributes>TrajectoryParticle
    132132--
    133133--
    … …  
    147147#Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration)
    148148#Thermostat_NoseHoover_init(int Step, double *delta_alpha)
    149 #Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration)</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2149</x><y>259</y><w>209</w><h>419</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;112;196;112;196;406</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1967</x><y>259</y><w>391</w><h>419</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;112;378;112;378;406</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1617</x><y>490</y><w>203</w><h>70</h></coordinates><panel_attributes>TrajectoryParticleInfo
     149#Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration)</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2149</x><y>343</y><w>209</w><h>419</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;112;196;112;196;406</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1967</x><y>343</y><w>391</w><h>419</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;112;378;112;378;406</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1617</x><y>574</y><w>203</w><h>70</h></coordinates><panel_attributes>TrajectoryParticleInfo
    150150--
    151151Trajectory: struct {vector&lt;Vector&gt; R,U,V}
    … …  
    153153--
    154154#TrajectoryParticleInfo()
    155 #~TrajectoryParticleInfo()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1757</x><y>539</y><w>601</w><h>139</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;105;588;105;588;126</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>539</y><w>34</w><h>146</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;133</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1519</x><y>574</y><w>244</w><h>111</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;56;231;56;231;98</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1736</x><y>364</y><w>147</w><h>112</h></coordinates><panel_attributes>TesselPoint
     155#~TrajectoryParticleInfo()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1757</x><y>623</y><w>601</w><h>139</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;105;588;105;588;126</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>623</y><w>34</w><h>146</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;133</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1519</x><y>658</y><w>244</w><h>111</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;56;231;56;231;98</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1736</x><y>448</y><w>147</w><h>112</h></coordinates><panel_attributes>TesselPoint
    156156--
    157157-id: Long
    … …  
    163163Responsibilities
    164164-- Resp1
    165 *-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>455</y><w>146</w><h>230</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>133;21;133;175;21;175;21;217</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>588</y><w>398</w><h>97</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>385;21;385;42;21;42;21;84</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>259</y><w>398</w><h>426</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>385;21;385;168;196;168;196;371;21;371;21;413</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>259</y><w>209</w><h>426</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>196;21;196;371;21;371;21;413</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>833</x><y>770</y><w>357</w><h>224</h></coordinates><panel_attributes>Bond
     165*-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>539</y><w>146</w><h>230</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>133;21;133;175;21;175;21;217</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>672</y><w>398</w><h>97</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>385;21;385;42;21;42;21;84</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>343</y><w>398</w><h>426</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>385;21;385;168;196;168;196;371;21;371;21;413</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>343</y><w>209</w><h>426</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>196;21;196;371;21;371;21;413</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>833</x><y>854</y><w>357</w><h>224</h></coordinates><panel_attributes>Bond
    166166--
    167167HydrogenBond: int
    … …  
    182182#bond()
    183183#bond(atom *left, atom *right, const int degree=1, const int number=0)
    184 #~bond()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1834</x><y>623</y><w>107</w><h>125</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    185 3</panel_attributes><additional_attributes>42;112;91;112;91;35;21;35;21;49</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1169</x><y>812</y><w>132</w><h>49</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    186 2</panel_attributes><additional_attributes>21;35;119;35</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>770</x><y>658</y><w>111</w><h>167</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    187 2</panel_attributes><additional_attributes>63;154;28;154;28;35;98;35;98;112</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1113</x><y>1246</y><w>504</w><h>168</h></coordinates><panel_attributes>BondGraph
     184#~bond()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1834</x><y>707</y><w>107</w><h>125</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     1853</panel_attributes><additional_attributes>42;112;91;112;91;35;21;35;21;49</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1169</x><y>896</y><w>132</w><h>49</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     1862</panel_attributes><additional_attributes>21;35;119;35</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>770</x><y>742</y><w>111</w><h>167</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     1872</panel_attributes><additional_attributes>63;154;28;154;28;35;98;35;98;112</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1113</x><y>1330</y><w>504</w><h>168</h></coordinates><panel_attributes>BondGraph
    188188--
    189189max_distance: double
    … …  
    199199                                                        double &amp;MinDistance, double &amp;MaxDistance, bool IsAngstroem)
    200200#CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker,
    201                                           double &amp;MinDistance, double &amp;MaxDistance, bool IsAngstroem)</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1596</x><y>1323</y><w>167</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;154;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1750</x><y>1281</y><w>147</w><h>133</h></coordinates><panel_attributes>MatrixContainer
     201                                          double &amp;MinDistance, double &amp;MaxDistance, bool IsAngstroem)</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1596</x><y>1407</y><w>167</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;154;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1750</x><y>1365</y><w>147</w><h>133</h></coordinates><panel_attributes>MatrixContainer
    202202--
    203203-id: Long
    … …  
    209209Responsibilities
    210210-- Resp1
    211 *-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>0</x><y>455</y><w>511</w><h>1050</h></coordinates><panel_attributes>config
     211*-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>0</x><y>539</y><w>511</w><h>1050</h></coordinates><panel_attributes>config
    212212--
    213213PsiType: int
    … …  
    297297#SetDefaultPath(const char * const path);
    298298#InitThermostats();
    299 #ParseThermostats(class ConfigFileBuffer * const fb);</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>490</x><y>1344</y><w>636</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;623;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1596</x><y>0</y><w>121</w><h>139</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    300 2</panel_attributes><additional_attributes>70;126;105;126;105;35;21;35;21;63</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2520</x><y>896</y><w>224</w><h>140</h></coordinates><panel_attributes>&lt;&lt;Singleton&gt;&gt;
     299#ParseThermostats(class ConfigFileBuffer * const fb);</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>490</x><y>1428</y><w>636</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;623;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1596</x><y>84</y><w>121</w><h>139</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     3002</panel_attributes><additional_attributes>70;126;105;126;105;35;21;35;21;63</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2520</x><y>980</y><w>224</w><h>140</h></coordinates><panel_attributes>&lt;&lt;Singleton&gt;&gt;
    301301errorLogger
    302302--
    … …  
    310310#static setVerbosity(int verbosityLevel);
    311311#protected errorLogger()
    312 #protected ~errorLogger()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2093</x><y>980</y><w>364</w><h>35</h></coordinates><panel_attributes>KeyCompare
     312#protected ~errorLogger()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2093</x><y>1064</y><w>364</w><h>35</h></coordinates><panel_attributes>KeyCompare
    313313--
    314314--
    315315#operator() (const KeySet SubgraphA, const KeySet SubgraphB) const: bool
    316 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1169</x><y>1134</y><w>147</w><h>105</h></coordinates><panel_attributes>UniqueFragments
     316</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1169</x><y>1218</y><w>147</w><h>105</h></coordinates><panel_attributes>UniqueFragments
    317317--
    318318ANOVAOrder: int
    … …  
    322322ShortestPathList: int *
    323323UsedList: bool **
    324 BondsPerSPCount: int *</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>490</x><y>1169</y><w>692</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>679;21;21;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1120</x><y>896</y><w>251</w><h>307</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>49;294;21;294;21;224;238;224;238;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>840</x><y>1043</y><w>245</w><h>28</h></coordinates><panel_attributes>Graph
     324BondsPerSPCount: int *</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>490</x><y>1253</y><w>692</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>679;21;21;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1120</x><y>980</y><w>251</w><h>307</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>49;294;21;294;21;224;238;224;238;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>840</x><y>1127</y><w>245</w><h>28</h></coordinates><panel_attributes>Graph
    325325{map &lt;KeySet, NumberValuePair, KeyCompare&gt;}
    326 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>861</x><y>1050</y><w>321</w><h>153</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>308;140;21;140;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>945</x><y>1106</y><w>56</w><h>28</h></coordinates><panel_attributes>KeySet
    327 {set&lt;int&gt;}</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>945</x><y>1113</y><w>237</w><h>90</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>224;77;21;77;21;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1085</x><y>973</y><w>99</w><h>230</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    328 0...N X 0...N</panel_attributes><additional_attributes>84;217;56;217;56;112;21;112;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1736</x><y>2198</y><w>147</w><h>42</h></coordinates><panel_attributes>LSQ_params
     326</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>861</x><y>1134</y><w>321</w><h>153</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>308;140;21;140;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>945</x><y>1190</y><w>56</w><h>28</h></coordinates><panel_attributes>KeySet
     327{set&lt;int&gt;}</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>945</x><y>1197</y><w>237</w><h>90</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>224;77;21;77;21;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1085</x><y>1057</y><w>99</w><h>230</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     3280...N X 0...N</panel_attributes><additional_attributes>84;217;56;217;56;112;21;112;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1736</x><y>2282</y><w>147</w><h>42</h></coordinates><panel_attributes>LSQ_params
    329329--
    330330vectors: const Vector **
    331331num: int
    332 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1043</x><y>182</y><w>147</w><h>35</h></coordinates><panel_attributes>lsq_params
    333 --
    334 x: gsl_vector *</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1169</x><y>182</y><w>118</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;105;21</additional_attributes></element></umlet_diagram>
     332</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1043</x><y>266</y><w>147</w><h>35</h></coordinates><panel_attributes>lsq_params
     333--
     334x: gsl_vector *</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1169</x><y>266</y><w>118</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;105;21</additional_attributes></element></umlet_diagram>

  • src/Actions/MapOfActions.cpp

    r51a5c8 rf0f1cc  
    4242#include "Actions/MoleculeAction/FillWithMoleculeAction.hpp"
    4343#include "Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp"
    44 #include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
    4544#include "Actions/MoleculeAction/SaveAdjacencyAction.hpp"
    4645#include "Actions/MoleculeAction/SaveBondsAction.hpp"
    4746#include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
    48 #include "Actions/MoleculeAction/SuspendInWaterAction.hpp"
    4947#include "Actions/MoleculeAction/TranslateAction.hpp"
    5048#include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
    … …  
    290288
    291289  // put action into each menu category
    292   MenuDescription["analysis"] = pair<std::string,std::string>("Analysis (pair correlation, volume)", "Analysis");
    293   MenuDescription["atom"] = pair<std::string,std::string>("Edit atoms", "Edit atoms");
    294   MenuDescription["command"] = pair<std::string,std::string>("Configuration", "Configuration");
    295   MenuDescription["fragmentation"] = pair<std::string,std::string>("Fragmentation", "Fragmentation");
    296   MenuDescription["molecule"] = pair<std::string,std::string>("Parse files into system", "Parse files");
    297   MenuDescription["parser"] = pair<std::string,std::string>("Edit molecules (load, parse, save)", "Edit molecules");
    298   MenuDescription["tesselation"] = pair<std::string,std::string>("Tesselate molecules", "Tesselate molecules");
    299   MenuDescription["world"] = pair<std::string,std::string>("Edit world", "Edit world");
    300 
    301290  MenuContainsActionMap.insert( pair<std::string, std::string> ("analysis", "molecular-volume") );
    302291  MenuContainsActionMap.insert( pair<std::string, std::string> ("analysis", "pair-correlation") );
    … …  
    456445  new MoleculeFillWithMoleculeAction();
    457446  new MoleculeLinearInterpolationofTrajectoriesAction();
    458   new MoleculeRotateToPrincipalAxisSystemAction();
    459447  new MoleculeSaveAdjacencyAction();
    460448  new MoleculeSaveBondsAction();
    461449  new MoleculeSaveTemperatureAction();
    462   new MoleculeSuspendInWaterAction();
    463450  new MoleculeTranslateAction();
    464451  new MoleculeVerletIntegrationAction();

  • src/Actions/MapOfActions.hpp

    r51a5c8 rf0f1cc  
    145145
    146146  std::multimap <std::string, std::string> MenuContainsActionMap;
    147   std::map <std::string, std::pair<std::string,std::string> > MenuDescription;
    148147
    149148  // instantiates and puts all known actions into the ActionRegistry

  • src/Actions/MoleculeAction/SuspendInWaterAction.cpp

    r51a5c8 rf0f1cc  
    5555  double volume = 0.;
    5656
    57   dialog->queryDouble(NAME, &density, MapOfActions::getInstance().getDescription(NAME));
    58   dialog->queryMolecule("molecule-by-id", &mol, MapOfActions::getInstance().getDescription("molecule-by-id"));
     57  dialog->queryMolecule(NAME, &mol, MapOfActions::getInstance().getDescription(NAME));
     58  dialog->queryDouble("density", &density, MapOfActions::getInstance().getDescription("density"));
    5959
    6060  if(dialog->display()) {

  • src/Actions/Process.cpp

    r51a5c8 rf0f1cc  
    4141
    4242int Process::getCurrStep(){
     43  OBSERVE;
    4344  return currStep;
    4445}
    4546
    4647void Process::setCurrStep(int _currStep){
    47   OBSERVE;
    4848  currStep = _currStep;
    4949}
    … …  
    5555    return 0;
    5656}
     57
    5758int Process::getMaxSteps(){
    5859  return maxSteps;

  • src/Actions/TesselationAction/ConvexEnvelopeAction.hpp

    r51a5c8 rf0f1cc  
    3131};
    3232
     33
    3334#endif // CONVEXENVELOPEACTION_HPP

  • src/Legacy/oldmenu.cpp

    r51a5c8 rf0f1cc  
    1010
    1111#include "Legacy/oldmenu.hpp"
    12 #include "analysis_bonds.hpp"
    1312#include "analysis_correlation.hpp"
    1413#include "World.hpp"
    … …  
    510509  Log() << Verbose(0) << " f - calculate temperature from current velocity" << endl;
    511510  Log() << Verbose(0) << " g - output all temperatures per step from velocities" << endl;
    512   Log() << Verbose(0) << " h - count the number of hydrogen bonds" << endl;
    513511  Log() << Verbose(0) << "all else - go back" << endl;
    514512  Log() << Verbose(0) << "===============================================" << endl;
    … …  
    599597        output->close();
    600598        delete(output);
    601       }
    602       break;
    603     case 'h':
    604       {
    605         int Z1;
    606         cout << "Please enter first interface element: ";
    607         cin >> Z1;
    608         const element * InterfaceElement = World::getInstance().getPeriode()->FindElement(Z1);
    609         int Z2;
    610         cout << "Please enter second interface element: ";
    611         cin >> Z2;
    612         const element * InterfaceElement2 = World::getInstance().getPeriode()->FindElement(Z2);
    613         cout << endl << "There are " << CountHydrogenBridgeBonds(World::getInstance().getMolecules(), InterfaceElement, InterfaceElement2) << " hydrogen bridges with connections to " << (InterfaceElement != 0 ? InterfaceElement->name : "None") << " and " << (InterfaceElement2 != 0 ? InterfaceElement2->name : "None") << "." << endl;
    614599      }
    615600      break;

  • src/Makefile.am

    r51a5c8 rf0f1cc  
    102102  Patterns/Singleton.hpp
    103103
    104 QTUIMOC_HEADER = UIElements/QT4/QTDialog.hpp \
    105                                  UIElements/QT4/QTMainWindow.hpp \
    106                                  UIElements/Menu/QT4/QTMenu.hpp \
    107                                  UIElements/Views/QT4/QTWorldView.hpp \
    108                                  UIElements/Views/QT4/GLMoleculeView.hpp \
    109                                  UIElements/Views/QT4/QTMoleculeView.hpp \
    110                                  UIElements/Views/QT4/QTStatusBar.hpp
    111  
    112 QTUIMOC_TARGETS = QTMainWindow.moc.cpp \
    113                       QTMenu.moc.cpp\
    114                       QTDialog.moc.cpp \
    115                       QTWorldView.moc.cpp \
    116                       GLMoleculeView.moc.cpp \
    117                       QTMoleculeView.moc.cpp \
    118                       QTStatusBar.moc.cpp
    119 
    120104DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
    121105  Descriptors/AtomIdDescriptor.cpp \
    … …  
    146130                                  Exceptions/SkewException.hpp \
    147131                                  Exceptions/ZeroVectorException.hpp
    148                                  
    149 QTUISOURCE = ${QTUIMOC_TARGETS} \
    150                          UIElements/QT4/QTMainWindow.cpp \
    151                          UIElements/QT4/QTDialog.cpp \
    152                          UIElements/QT4/QTUIFactory.cpp \
    153                          UIElements/Menu/QT4/QTMenu.cpp \
    154                          UIElements/Views/QT4/QTWorldView.cpp \
    155                          UIElements/Views/QT4/GLMoleculeView.cpp \
    156                          UIElements/Views/QT4/QTMoleculeView.cpp \
    157                          UIElements/Views/QT4/QTStatusBar.cpp
    158              
    159 QTUIHEADER = ${QTUIMOC_HEADER} UIElements/QT4/QTUIFactory.hpp
    160 
    161 QTUI_DEFS =
    162132
    163133SOURCE = \
    … …  
    257227
    258228BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
    259 GUI_LIBS = ${QT_LDADD} ${QT_LIB_GUI} -lQtOpenGL ${GLU_LIBS}
    260229INCLUDES = -I$(top_srcdir)/src/unittests -I$(top_srcdir)/src/Actions -I$(top_srcdir)/src/UIElements
    261230
    262 noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a libmenu.a libparser.a
    263 bin_PROGRAMS = molecuilder molecuildergui joiner analyzer
    264 
     231noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a libparser.a
     232bin_PROGRAMS = molecuilder joiner analyzer
    265233molecuilderdir = ${bindir}
    266 
    267234libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
    268 
    269 libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER}
    270235libparser_a_SOURCES = ${PARSERSOURCE} ${PARSERHEADER}
    271236libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
    272 
    273237molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
    274 
    275 molecuilder_CXXFLAGS = $(BOOST_CPPFLAGS)
    276 #molecuilder_CXXFLAGS += -DNO_CACHING
    277 molecuilder_LDFLAGS = $(BOOST_LIB)
    278 molecuilder_SOURCES = ${LEGACYSOURCE} builder.cpp
    279 molecuilder_SOURCES += $(srcdir)/version.c
    280 molecuilder_LDADD = UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilder.a libparser.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
    281 
    282 #Stuff for building the GUI using QT
    283 molecuildergui_SOURCES = ${QTUISOURCE} ${LEGACYSOURCE} builder.cpp
    284 molecuildergui_SOURCES += $(srcdir)/version.c
    285 molecuildergui_CXXFLAGS = ${QT_CXXFLAGS} ${GLU_CXXFLAGS} -DUSE_GUI_QT
    286 molecuildergui_LDFLAGS = $(BOOST_LIB) ${QT_LDFLAGS} ${GLU_LDFLAGS}
    287 molecuildergui_LDADD = UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilder.a libparser.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}  ${GUI_LIBS}
    288 
     238molecuilder_LDFLAGS = $(BOOST_LDFLAGS)
     239molecuilder_SOURCES = builder.cpp
     240molecuilder_LDADD =  UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilder.a libparser.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
    289241joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
    290242joiner_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    291 
    292243analyzer_SOURCES = analyzer.cpp datacreator.cpp parser.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp
    293244analyzer_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    294 
    295 #Rules needed for QT4
    296 # UI-Files are scattered throughout several subdirectories
    297 # Therfore `%'-rules do not seem to work
    298 #Quick fix to get it done otherwise
    299 ${QTUIMOC_TARGETS}: ${QTUIMOC_HEADER}
    300         list='$(QTUIMOC_HEADER)'; for header in $$list; do \
    301         echo "Making mocfile for $$header"; \
    302         target=`basename $$header | sed "s/\(.*\)\..*/\1.moc.cpp/"`;\
    303         $(MOC) $(srcdir)/$$header -o $$target \
    304         || eval $$failcom; \
    305         done;
    306 
    307 MOSTLYCLEANFILES = ${QTUIMOC_TARGETS}
    308        
    309 #EXTRA_DIST = ${molecuilder_DATA}
    310245
    311246FORCE:
    … …  
    323258        echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
    324259
    325 
     260molecuilder_SOURCES += $(srcdir)/version.c

  • src/UIElements/Dialog.cpp

    r51a5c8 rf0f1cc  
    3434
    3535bool Dialog::display(){
    36   if(checkAll()){
    37     setAll();
    38     return true;
    39   }
    40   else{
    41     return false;
    42   }
    43 }
    44 
    45 bool Dialog::checkAll(){
    4636  list<Query*>::iterator iter;
    4737  bool retval = true;
    … …  
    5444    }
    5545  }
     46  if (retval){
     47    // if all queries succeeded we can set the targets to appropriate values
     48    for(iter=queries.begin(); iter!=queries.end(); iter++) {
     49      (*iter)->setResult();
     50    }
     51  }
    5652  return retval;
    57 }
    58 
    59 void Dialog::setAll(){
    60   list<Query*>::iterator iter;
    61   for(iter=queries.begin(); iter!=queries.end(); iter++) {
    62     (*iter)->setResult();
    63   }
    6453}
    6554

  • src/UIElements/Dialog.hpp

    r51a5c8 rf0f1cc  
    3636
    3737  virtual bool display();
    38 
    39   virtual bool checkAll();
    40   virtual void setAll();
    4138
    4239protected:

  • src/UIElements/MainWindow.cpp

    r51a5c8 rf0f1cc  
    1111
    1212MainWindow::MainWindow()
    13 {}
     13{
     14  // TODO Auto-generated constructor stub
     15
     16}
    1417
    1518MainWindow::~MainWindow()
    16 {}
     19{
     20  // TODO Auto-generated destructor stub
     21}

  • src/UIElements/TextUI/TextUIFactory.cpp

    r51a5c8 rf0f1cc  
    99#include "UIElements/TextUI/TextWindow.hpp"
    1010#include "UIElements/TextUI/TextDialog.hpp"
     11
    1112
    1213TextUIFactory::TextUIFactory()

  • src/UIElements/TextUI/TextUIFactory.hpp

    r51a5c8 rf0f1cc  
    1313class TextUIFactory : public UIFactory
    1414{
    15   friend class UIFactory;
     15friend class UIFactory;
    1616
    1717public:

  • src/UIElements/TextUI/TextWindow.cpp

    r51a5c8 rf0f1cc  
    2525#include "Views/StreamStringView.hpp"
    2626#include "Views/MethodStringView.hpp"
    27 #include "Helpers/MemDebug.hpp"
    2827
    2928#include "defs.hpp"
    … …  
    7170  new ActionMenuItem('a',"set molecule (in)active",main_menu,setMoleculeAction);
    7271
    73   TextMenu *Menu = NULL;
    74   std::set <char> ShortcutList;
    75   for(map<std::string, pair<std::string,std::string> >::iterator iter = MapOfActions::getInstance().MenuDescription.begin(); iter != MapOfActions::getInstance().MenuDescription.end(); ++iter) {
    76     Menu = new TextMenu(Log() << Verbose(0), iter->second.second);
    77     NametoTextMenuMap.insert( pair <std::string, TextMenu *> (iter->first, Menu) );
    78     new SubMenuItem(getSuitableShortForm(ShortcutList,iter->first),iter->second.first.c_str(),main_menu,Menu);
    79   }
     72  TextMenu *AnalysisMenu = new TextMenu(Log() << Verbose(0), "Analysis");
     73  NametoTextMenuMap.insert( pair <std::string, TextMenu *> ("analysis", AnalysisMenu) );
     74  new SubMenuItem('A',"Analysis (pair correlation, volume)",main_menu,AnalysisMenu);
     75
     76  TextMenu *CommandMenu = new TextMenu(Log() << Verbose(0), "Configuration");
     77  NametoTextMenuMap.insert( pair <std::string, TextMenu *> ("command", CommandMenu) );
     78  new SubMenuItem('c',"configuration",main_menu,CommandMenu);
     79
     80  TextMenu *AtomMenu = new TextMenu(Log() << Verbose(0), "Atoms");
     81  NametoTextMenuMap.insert( pair <std::string, TextMenu *> ("atom", AtomMenu) );
     82  new SubMenuItem('e',"edit atoms",main_menu,AtomMenu);
     83
     84  TextMenu *FragmentationMenu = new TextMenu(Log() << Verbose(0), "Fragmentation");
     85  NametoTextMenuMap.insert( pair <std::string, TextMenu *> ("fragmentation", FragmentationMenu) );
     86  new SubMenuItem('f',"fragmentation",main_menu,FragmentationMenu);
     87
     88  TextMenu *ParserMenu = new TextMenu(Log() << Verbose(0), "Parse files");
     89  NametoTextMenuMap.insert( pair <std::string, TextMenu *> ("parser", ParserMenu) );
     90  new SubMenuItem('p',"parse files into system",main_menu,ParserMenu);
     91
     92  TextMenu *MoleculesMenu = new TextMenu(Log() << Verbose(0), "Edit Molecules");
     93  NametoTextMenuMap.insert( pair <std::string, TextMenu *> ("analysis", AnalysisMenu) );
     94  new SubMenuItem('m',"edit molecules (load, parse, save)",main_menu,MoleculesMenu);
     95
     96  TextMenu *TesselationMenu = new TextMenu(Log() << Verbose(0), "Tesselate Molecules");
     97  NametoTextMenuMap.insert( pair <std::string, TextMenu *> ("tesselation", TesselationMenu) );
     98  new SubMenuItem('t',"tesselate molecules",main_menu,TesselationMenu);
     99
     100  TextMenu *WorldMenu = new TextMenu(Log() << Verbose(0), "World");
     101  NametoTextMenuMap.insert( pair <std::string, TextMenu *> ("world", WorldMenu) );
     102  new SubMenuItem('w',"edit world",main_menu,WorldMenu);
    80103
    81104  new SeperatorItem(main_menu);

  • src/UIElements/UIFactory.cpp

    r51a5c8 rf0f1cc  
    1212#include "UIElements/UIFactory.hpp"
    1313#include "Helpers/Assert.hpp"
    14 #include "Helpers/MemDebug.hpp"
    1514
    1615using namespace std;

  • src/UIElements/UIFactory.hpp

    r51a5c8 rf0f1cc  
    3030  friend class Singleton<UIFactory,false>;
    3131public:
    32 
    3332  /**
    3433   * Produce some kind of main window, of whichever type was chosen when the factory was created

  • src/analysis_bonds.cpp

    r51a5c8 rf0f1cc  
    121121 * \param *molecules molecules to count bonds
    122122 * \param *InterfaceElement or NULL
    123  * \param *Interface2Element or NULL
    124  */
    125 int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL, const element * Interface2Element = NULL)
     123 */
     124int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL)
    126125{
    127126  int count = 0;
    … …  
    129128  double Otherangle = 0.;
    130129  bool InterfaceFlag = false;
    131   bool Interface2Flag = false;
    132130  bool OtherHydrogenFlag = true;
    133131  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); ++MolWalker) {
    … …  
    147145              OtherHydrogens = 0;
    148146              InterfaceFlag = (InterfaceElement == NULL);
    149               Interface2Flag = (Interface2Element == NULL);
    150147              for (BondList::const_iterator BondRunner = (*Runner)->ListOfBonds.begin(); BondRunner != (*Runner)->ListOfBonds.end(); BondRunner++) {
    151148                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Runner);
    … …  
    158155                }
    159156                InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
    160                 Interface2Flag = Interface2Flag || (OtherAtom->type == Interface2Element);
    161157              }
    162158              DoLog(1) && (Log() << Verbose(1) << "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens." << endl);
    … …  
    172168                  break;
    173169              }
    174               if (InterfaceFlag && Interface2Flag && OtherHydrogenFlag) {
     170              if (InterfaceFlag && OtherHydrogenFlag) {
    175171                // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
    176172                for (BondList::const_iterator BondRunner = (*Walker)->ListOfBonds.begin(); BondRunner != (*Walker)->ListOfBonds.end(); BondRunner++) {

  • src/analysis_bonds.hpp

    r51a5c8 rf0f1cc  
    3333void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, const element *type1, const element *type2, double &Min, double &Mean, double &Max);
    3434
    35 int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, const element * InterfaceElement, const element * Interface2Element);
     35int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, const element * InterfaceElement);
    3636int CountBondsOfTwo(MoleculeListClass * const molecules, const element * const first, const element * const second);
    3737int CountBondsOfThree(MoleculeListClass * const molecules, const element * const first, const element * const second, const element * const third);

  • src/boundary.cpp

    r51a5c8 rf0f1cc  
    10041004//  // Purges surplus triangles.
    10051005//  TesselStruct->RemoveDegeneratedTriangles();
    1006 //
    1007 //  // check envelope for consistency
    1008 //  status = CheckListOfBaselines(TesselStruct);
     1006
     1007  // check envelope for consistency
     1008  status = CheckListOfBaselines(TesselStruct);
    10091009
    10101010  cout << "before correction" << endl;

  • src/builder.cpp

    r51a5c8 rf0f1cc  
    6060#include "config.hpp"
    6161#include "log.hpp"
    62 #include "memoryusageobserver.hpp"
    63 #include "molecule.hpp"
    64 #include "periodentafel.hpp"
    65 #include "tesselationhelpers.hpp"
    66 #include "UIElements/UIFactory.hpp"
    67 #include "UIElements/TextUI/TextUIFactory.hpp"
    68 #include "UIElements/CommandLineUI/CommandLineUIFactory.hpp"
    69 #ifdef USE_GUI_QT
    70 #include "UIElements/QT4/QTUIFactory.hpp"
    71 #endif
    72 #include "UIElements/MainWindow.hpp"
    73 #include "UIElements/Dialog.hpp"
    74 #include "Menu/ActionMenuItem.hpp"
    7562#include "verbose.hpp"
    7663#include "World.hpp"
    … …  
    159146      UIFactory::makeUserInterface("CommandLine");
    160147    } else {
    161       #ifdef USE_GUI_QT
    162         DoLog(0) && (Log() << Verbose(0) << "Setting UI to QT4." << endl);
    163         UIFactory::registerFactory(new QTUIFactory::description());
    164         UIFactory::makeUserInterface("QT4");
    165       #else
    166         DoLog(0) && (Log() << Verbose(0) << "Setting UI to Text." << endl);
    167         cout << ESPACKVersion << endl;
    168         UIFactory::registerFactory(new TextUIFactory::description());
    169         UIFactory::makeUserInterface("Text");
    170       #endif
     148      DoLog(0) && (Log() << Verbose(0) << "Setting UI to Text." << endl);
     149      UIFactory::registerFactory(new TextUIFactory::description());
     150      UIFactory::makeUserInterface("Text");
    171151    }
    172152  }

  • src/defs.hpp

    r51a5c8 rf0f1cc  
    8282#define STD_SEPERATOR_SPACER '-'
    8383
    84 #define MOLECUILDER_NAME "Molecuilder"
    85 
    8684#endif /*DEFS_HPP_*/

  • src/molecule.hpp

    r51a5c8 rf0f1cc  
    2929#include <string>
    3030
    31 #include "types.hpp"
     31#include "defs.hpp"
    3232#include "graph.hpp"
    3333#include "stackclass.hpp"

  • src/tesselation.cpp

    r51a5c8 rf0f1cc  
    231231{
    232232  Info FunctionInfo(__func__);
    233   double angle = CalculateConvexity();
    234   if (angle > -MYEPSILON) {
    235     DoLog(0) && (Log() << Verbose(0) << "ACCEPT: Angle is greater than pi: convex." << endl);
    236     return true;
    237   } else {
    238     DoLog(0) && (Log() << Verbose(0) << "REJECT: Angle is less than pi: concave." << endl);
    239     return false;
    240   }
    241 }
    242 
    243 
    244 /** Calculates the angle between two triangles with respect to their normal vector.
    245  * We sum the two angles of each height vector with respect to the center of the baseline.
    246  * \return angle > 0 then convex, if < 0 then concave
    247  */
    248 double BoundaryLineSet::CalculateConvexity() const
    249 {
    250   Info FunctionInfo(__func__);
    251233  Vector BaseLineCenter, BaseLineNormal, BaseLine, helper[2], NormalCheck;
    252234  // get the two triangles
    … …  
    297279  BaseLineNormal.Scale(-1.);
    298280  double angle = GetAngle(helper[0], helper[1], BaseLineNormal);
    299   return (angle - M_PI);
     281  if ((angle - M_PI) > -MYEPSILON) {
     282    DoLog(0) && (Log() << Verbose(0) << "ACCEPT: Angle is greater than pi: convex." << endl);
     283    return true;
     284  } else {
     285    DoLog(0) && (Log() << Verbose(0) << "REJECT: Angle is less than pi: concave." << endl);
     286    return false;
     287  }
    300288}
    301289
    … …  
    316304/** Returns other endpoint of the line.
    317305 * \param *point other endpoint
    318  * \return NULL - if endpoint not contained in BoundaryLineSet::lines, or pointer to BoundaryPointSet otherwise
     306 * \return NULL - if endpoint not contained in BoundaryLineSet, or pointer to BoundaryPointSet otherwise
    319307 */
    320308class BoundaryPointSet *BoundaryLineSet::GetOtherEndpoint(const BoundaryPointSet * const point) const
    … …  
    327315  else
    328316    return NULL;
    329 }
    330 ;
    331 
    332 /** Returns other triangle of the line.
    333  * \param *point other endpoint
    334  * \return NULL - if triangle not contained in BoundaryLineSet::triangles, or pointer to BoundaryTriangleSet otherwise
    335  */
    336 class BoundaryTriangleSet *BoundaryLineSet::GetOtherTriangle(const BoundaryTriangleSet * const triangle) const
    337 {
    338   Info FunctionInfo(__func__);
    339   if (triangles.size() == 2) {
    340     for (TriangleMap::const_iterator TriangleRunner = triangles.begin(); TriangleRunner != triangles.end(); ++TriangleRunner)
    341       if (TriangleRunner->second != triangle)
    342         return TriangleRunner->second;
    343   }
    344   return NULL;
    345317}
    346318;
    … …  
    689661;
    690662
    691 /** Returns the baseline which does not contain the given boundary point \a *point.
    692  * \param *point endpoint which is neither endpoint of the desired line
    693  * \return pointer to desired third baseline
    694  */
    695 class BoundaryLineSet *BoundaryTriangleSet::GetThirdLine(const BoundaryPointSet * const point) const
    696 {
    697   Info FunctionInfo(__func__);
    698   // sanity check
    699   if (!ContainsBoundaryPoint(point))
    700     return NULL;
    701   for (int i = 0; i < 3; i++)
    702     if (!lines[i]->ContainsBoundaryPoint(point))
    703       return lines[i];
    704   // actually, that' impossible :)
    705   return NULL;
    706 }
    707 ;
    708 
    709663/** Calculates the center point of the triangle.
    710664 * Is third of the sum of all endpoints.
    … …  
    11561110    TesselPointList *ListofPoints = LC->GetPointsInsideSphere(RADIUS, (*VRunner));
    11571111
    1158     DoLog(1) && (Log() << Verbose(1) << "The following atoms are inside sphere at " << (*VRunner) << ":" << endl);
     1112    DoLog(1) && (Log() << Verbose(1) << "The following atoms are inside sphere at " << OtherOptCenter << ":" << endl);
    11591113    for (TesselPointList::const_iterator Runner = ListofPoints->begin(); Runner != ListofPoints->end(); ++Runner)
    1160       DoLog(1) && (Log() << Verbose(1) << "  " << *(*Runner) << " with distance " << (*Runner)->node->distance(*(*VRunner)) << "." << endl);
     1114      DoLog(1) && (Log() << Verbose(1) << "  " << *(*Runner) << " with distance " << (*Runner)->node->distance(OtherOptCenter) << "." << endl);
    11611115
    11621116    // remove baseline's endpoints and candidates
    … …  
    11741128      DoeLog(1) && (eLog() << Verbose(1) << "External atoms inside of sphere at " << *(*VRunner) << ":" << endl);
    11751129      for (TesselPointList::const_iterator Runner = ListofPoints->begin(); Runner != ListofPoints->end(); ++Runner)
    1176         DoeLog(1) && (eLog() << Verbose(1) << "  " << *(*Runner) << " at distance " << setprecision(13) << (*Runner)->node->distance(*(*VRunner)) << setprecision(6) << "." << endl);
    1177 
    1178       // check with animate_sphere.tcl VMD script
    1179       if (ThirdPoint != NULL) {
    1180         DoeLog(1) && (eLog() << Verbose(1) << "Check by: animate_sphere 0 " << BaseLine->endpoints[0]->Nr + 1 << " " << BaseLine->endpoints[1]->Nr + 1 << " " << ThirdPoint->Nr + 1 << " " << RADIUS << " " << OldCenter[0] << " " << OldCenter[1] << " " << OldCenter[2] << " " << (*VRunner)->at(0) << " " << (*VRunner)->at(1) << " " << (*VRunner)->at(2) << endl);
    1181       } else {
    1182         DoeLog(1) && (eLog() << Verbose(1) << "Check by: ... missing third point ..." << endl);
    1183         DoeLog(1) && (eLog() << Verbose(1) << "Check by: animate_sphere 0 " << BaseLine->endpoints[0]->Nr + 1 << " " << BaseLine->endpoints[1]->Nr + 1 << " ??? " << RADIUS << " " << OldCenter[0] << " " << OldCenter[1] << " " << OldCenter[2] << " " << (*VRunner)->at(0) << " " << (*VRunner)->at(1) << " " << (*VRunner)->at(2) << endl);
    1184       }
     1130        DoeLog(1) && (eLog() << Verbose(1) << "  " << *(*Runner) << endl);
    11851131    }
    11861132    delete (ListofPoints);
    11871133
     1134    // check with animate_sphere.tcl VMD script
     1135    if (ThirdPoint != NULL) {
     1136      DoLog(1) && (Log() << Verbose(1) << "Check by: animate_sphere 0 " << BaseLine->endpoints[0]->Nr + 1 << " " << BaseLine->endpoints[1]->Nr + 1 << " " << ThirdPoint->Nr + 1 << " " << RADIUS << " " << OldCenter[0] << " " << OldCenter[1] << " " << OldCenter[2] << " " << (*VRunner)->at(0) << " " << (*VRunner)->at(1) << " " << (*VRunner)->at(2) << endl);
     1137    } else {
     1138      DoLog(1) && (Log() << Verbose(1) << "Check by: ... missing third point ..." << endl);
     1139      DoLog(1) && (Log() << Verbose(1) << "Check by: animate_sphere 0 " << BaseLine->endpoints[0]->Nr + 1 << " " << BaseLine->endpoints[1]->Nr + 1 << " ??? " << RADIUS << " " << OldCenter[0] << " " << OldCenter[1] << " " << OldCenter[2] << " " << (*VRunner)->at(0) << " " << (*VRunner)->at(1) << " " << (*VRunner)->at(2) << endl);
     1140    }
    11881141  }
    11891142  return flag;
    … …  
    33373290                        }
    33383291                      } else {
    3339                         DoeLog(0) && (eLog() << Verbose(1) << "REJECT: Distance to center of circumcircle is not the same from each corner of the triangle: " << fabs(radius - otherradius) << endl);
     3292                        DoLog(1) && (Log() << Verbose(1) << "REJECT: Distance to center of circumcircle is not the same from each corner of the triangle: " << fabs(radius - otherradius) << endl);
    33403293                      }
    33413294                    } else {
    … …  
    46374590
    46384591  DoLog(0) && (Log() << Verbose(0) << "FindAllDegeneratedTriangles() found " << DegeneratedTriangles->size() << " triangles:" << endl);
    4639   for (IndexToIndex::iterator it = DegeneratedTriangles->begin(); it != DegeneratedTriangles->end(); it++)
     4592  IndexToIndex::iterator it;
     4593  for (it = DegeneratedTriangles->begin(); it != DegeneratedTriangles->end(); it++)
    46404594    DoLog(0) && (Log() << Verbose(0) << (*it).first << " => " << (*it).second << endl);
    46414595
    … …  
    46554609  int count = 0;
    46564610
    4657   // iterate over all degenerated triangles
    4658   for (IndexToIndex::iterator TriangleKeyRunner = DegeneratedTriangles->begin(); !DegeneratedTriangles->empty(); TriangleKeyRunner = DegeneratedTriangles->begin()) {
    4659     DoLog(0) && (Log() << Verbose(0) << "Checking presence of triangles " << TriangleKeyRunner->first << " and " << TriangleKeyRunner->second << "." << endl);
    4660     // both ways are stored in the map, only use one
    4661     if (TriangleKeyRunner->first > TriangleKeyRunner->second)
    4662       continue;
    4663 
    4664     // determine from the keys in the map the two _present_ triangles
     4611  for (IndexToIndex::iterator TriangleKeyRunner = DegeneratedTriangles->begin(); TriangleKeyRunner != DegeneratedTriangles->end(); ++TriangleKeyRunner) {
    46654612    finder = TrianglesOnBoundary.find(TriangleKeyRunner->first);
    46664613    if (finder != TrianglesOnBoundary.end())
    46674614      triangle = finder->second;
    46684615    else
    4669       continue;
     4616      break;
    46704617    finder = TrianglesOnBoundary.find(TriangleKeyRunner->second);
    46714618    if (finder != TrianglesOnBoundary.end())
    46724619      partnerTriangle = finder->second;
    46734620    else
    4674       continue;
    4675 
    4676     // determine which lines are shared by the two triangles
     4621      break;
     4622
    46774623    bool trianglesShareLine = false;
    46784624    for (int i = 0; i < 3; ++i)

  • src/tesselation.hpp

    r51a5c8 rf0f1cc  
    138138    bool ContainsBoundaryPoint(const BoundaryPointSet * const point) const;
    139139    bool CheckConvexityCriterion() const;
    140     double CalculateConvexity() const;
    141140    class BoundaryPointSet *GetOtherEndpoint(const BoundaryPointSet * const point) const;
    142     class BoundaryTriangleSet *GetOtherTriangle(const BoundaryTriangleSet * const triangle) const;
    143141
    144142    class BoundaryPointSet *endpoints[2];
    … …  
    166164    bool ContainsBoundaryPoint(const TesselPoint * const point) const;
    167165    class BoundaryPointSet *GetThirdEndpoint(const BoundaryLineSet * const line) const;
    168     class BoundaryLineSet *GetThirdLine(const BoundaryPointSet * const point) const;
    169166    bool IsPresentTupel(const BoundaryPointSet * const Points[3]) const;
    170167    bool IsPresentTupel(const BoundaryTriangleSet * const T) const;

  • src/tesselationhelpers.cpp

    r51a5c8 rf0f1cc  
    1212#include "info.hpp"
    1313#include "linkedcell.hpp"
    14 #include "linearsystemofequations.hpp"
    1514#include "log.hpp"
    1615#include "tesselation.hpp"
    … …  
    186185  beta = M_PI - SideC.Angle(SideA);
    187186  gamma = M_PI - SideA.Angle(SideB);
    188   Log() << Verbose(1) << "INFO: alpha = " << alpha/M_PI*180. << ", beta = " << beta/M_PI*180. << ", gamma = " << gamma/M_PI*180. << "." << endl;
     187  //Log() << Verbose(1) << "INFO: alpha = " << alpha/M_PI*180. << ", beta = " << beta/M_PI*180. << ", gamma = " << gamma/M_PI*180. << "." << endl;
    189188  if (fabs(M_PI - alpha - beta - gamma) > HULLEPSILON) {
    190189    DoeLog(2) && (eLog()<< Verbose(2) << "GetCenterofCircumcircle: Sum of angles " << (alpha+beta+gamma)/M_PI*180. << " > 180 degrees by " << fabs(M_PI - alpha - beta - gamma)/M_PI*180. << "!" << endl);
    … …  
    199198  (*Center) += helper;
    200199  Center->Scale(1./(sin(2.*alpha) + sin(2.*beta) + sin(2.*gamma)));
    201   Log() << Verbose(1) << "INFO: Center (1st algo) is at " << *Center << "." << endl;
    202 
    203 //  LinearSystemOfEquations LSofEq(NDIM,NDIM);
    204 //  double *matrix = new double[NDIM*NDIM];
    205 //  matrix[0] = 0.;
    206 //  matrix[1] = a.DistanceSquared(b);
    207 //  matrix[2] = a.DistanceSquared(c);
    208 //  matrix[3] = a.DistanceSquared(b);
    209 //  matrix[4] = 0.;
    210 //  matrix[5] = b.DistanceSquared(c);
    211 //  matrix[6] = a.DistanceSquared(c);
    212 //  matrix[7] = b.DistanceSquared(c);
    213 //  matrix[8] = 0.;
    214 //  cout << "Matrix is: ";
    215 //  for (int i=0;i<NDIM*NDIM;i++)
    216 //    cout << matrix[i] << "\t";
    217 //  cout << endl;
    218 //  LSofEq.SetA(matrix);
    219 //  delete[](matrix);
    220 //  LSofEq.Setb(new Vector(1.,1.,1.));
    221 //  LSofEq.SetSymmetric(true);
    222 //  helper.Zero();
    223 //  if (!LSofEq.GetSolutionAsVector(helper)) {
    224 //    DoLog(0) && (eLog()<< Verbose(0) << "Could not solve the linear system in GetCenterofCircumCircle()!" << endl);
    225 //  }
    226 //  cout << "Solution is " << helper << endl;
    227   // is equivalent to the three lines below
    228   helper[0] = SideA.NormSquared()*(SideB.NormSquared()+SideC.NormSquared() - SideA.NormSquared());
    229   helper[1] = SideB.NormSquared()*(SideC.NormSquared()+SideA.NormSquared() - SideB.NormSquared());
    230   helper[2] = SideC.NormSquared()*(SideA.NormSquared()+SideB.NormSquared() - SideC.NormSquared());
    231 
    232   Center->Zero();
    233   *Center += helper[0] * a;
    234   *Center += helper[1] * b;
    235   *Center += helper[2] * c;
    236   Center->Scale(1./(helper[0]+helper[1]+helper[2]));
    237   Log() << Verbose(1) << "INFO: Center (2nd algo) is at " << *Center << "." << endl;
    238200};
    239201
    … …  
    457419/** Calculates the volume of a general tetraeder.
    458420 * \param *a first vector
    459  * \param *b second vector
    460  * \param *c third vector
    461  * \param *d fourth vector
     421 * \param *a first vector
     422 * \param *a first vector
     423 * \param *a first vector
    462424 * \return \f$ \frac{1}{6} \cdot ((a-d) \times (a-c) \cdot  (a-b)) \f$
    463425 */
    … …  
    477439  volume = 1./6. * fabs(Point.ScalarProduct(TetraederVector[2]));
    478440  return volume;
    479 };
    480 
    481 /** Calculates the area of a general triangle.
    482  * We use the Heron's formula of area, [Bronstein, S. 138]
    483  * \param &A first vector
    484  * \param &B second vector
    485  * \param &C third vector
    486  * \return \f$ \frac{1}{6} \cdot ((a-d) \times (a-c) \cdot  (a-b)) \f$
    487  */
    488 double CalculateAreaofGeneralTriangle(const Vector &A, const Vector &B, const Vector &C)
    489 {
    490   Info FunctionInfo(__func__);
    491 
    492   const double sidea = B.distance(C);
    493   const double sideb = A.distance(C);
    494   const double sidec = A.distance(B);
    495   const double s = (sidea+sideb+sidec)/2.;
    496 
    497   const double area = sqrt(s*(s-sidea)*(s-sideb)*(s-sidec));
    498   return area;
    499441};
    500442
    … …  
    940882  class BoundaryPointSet *point = NULL;
    941883  class BoundaryLineSet *line = NULL;
    942   class BoundaryTriangleSet *triangle = NULL;
    943   double ConcavityPerLine = 0.;
    944   double ConcavityPerTriangle = 0.;
    945   double area = 0.;
    946   double totalarea = 0.;
    947 
     884
     885  // calculate remaining concavity
    948886  for (PointMap::const_iterator PointRunner = TesselStruct->PointsOnBoundary.begin(); PointRunner != TesselStruct->PointsOnBoundary.end(); PointRunner++) {
    949887    point = PointRunner->second;
    950888    DoLog(1) && (Log() << Verbose(1) << "INFO: Current point is " << *point << "." << endl);
    951 
    952     // calculate mean concavity over all connected line
    953     ConcavityPerLine = 0.;
     889    point->value = 0;
    954890    for (LineMap::iterator LineRunner = point->lines.begin(); LineRunner != point->lines.end(); LineRunner++) {
    955891      line = LineRunner->second;
    956892      //Log() << Verbose(1) << "INFO: Current line of point " << *point << " is " << *line << "." << endl;
    957       ConcavityPerLine -= line->CalculateConvexity();
    958     }
    959     ConcavityPerLine /= point->lines.size();
    960 
    961     // weigh with total area of the surrounding triangles
    962     totalarea  = 0.;
    963     TriangleSet *triangles = TesselStruct->GetAllTriangles(PointRunner->second);
    964     for (TriangleSet::iterator TriangleRunner = triangles->begin(); TriangleRunner != triangles->end(); ++TriangleRunner) {
    965       totalarea += CalculateAreaofGeneralTriangle(*(*TriangleRunner)->endpoints[0]->node->node, *(*TriangleRunner)->endpoints[1]->node->node, *(*TriangleRunner)->endpoints[2]->node->node);
    966     }
    967     ConcavityPerLine *= totalarea;
    968 
    969     // calculate mean concavity over all attached triangles
    970     ConcavityPerTriangle = 0.;
    971     for (TriangleSet::const_iterator TriangleRunner = triangles->begin(); TriangleRunner != triangles->end(); ++TriangleRunner) {
    972       line = (*TriangleRunner)->GetThirdLine(PointRunner->second);
    973       triangle = line->GetOtherTriangle(*TriangleRunner);
    974       area = CalculateAreaofGeneralTriangle(*triangle->endpoints[0]->node->node, *triangle->endpoints[1]->node->node, *triangle->endpoints[2]->node->node);
    975       area += CalculateAreaofGeneralTriangle(*(*TriangleRunner)->endpoints[0]->node->node, *(*TriangleRunner)->endpoints[1]->node->node, *(*TriangleRunner)->endpoints[2]->node->node);
    976       area *= -line->CalculateConvexity();
    977       if (area > 0)
    978         ConcavityPerTriangle += area;
    979 //      else
    980 //        ConcavityPerTriangle -= area;
    981     }
    982     ConcavityPerTriangle /= triangles->size()/totalarea;
    983     delete(triangles);
    984 
    985     // add up
    986     point->value = ConcavityPerLine + ConcavityPerTriangle;
    987   }
    988 };
    989 
    990 
    991 
    992 /** Calculates the concavity for each of the BoundaryPointSet's in a Tesselation.
    993  * Sets BoundaryPointSet::value equal to the nearest distance to convex envelope.
    994  * \param *out output stream for debugging
    995  * \param *TesselStruct pointer to Tesselation structure
    996  * \param *Convex pointer to convex Tesselation structure as reference
    997  */
    998 void CalculateConstrictionPerBoundaryPoint(const Tesselation * const TesselStruct, const Tesselation * const Convex)
    999 {
    1000   Info FunctionInfo(__func__);
    1001   double distance = 0.;
    1002 
    1003   for (PointMap::const_iterator PointRunner = TesselStruct->PointsOnBoundary.begin(); PointRunner != TesselStruct->PointsOnBoundary.end(); PointRunner++) {
    1004     DoeLog(1) && (eLog() << Verbose(1) << "INFO: Current point is " << * PointRunner->second << "." << endl);
    1005 
    1006     distance = 0.;
    1007     for (TriangleMap::const_iterator TriangleRunner = Convex->TrianglesOnBoundary.begin(); TriangleRunner != Convex->TrianglesOnBoundary.end(); TriangleRunner++) {
    1008       const double CurrentDistance = Convex->GetDistanceSquaredToTriangle(*PointRunner->second->node->node, TriangleRunner->second);
    1009       if (CurrentDistance < distance)
    1010         distance = CurrentDistance;
    1011     }
    1012 
    1013     PointRunner->second->value = distance;
    1014   }
    1015 };
     893      if (!line->CheckConvexityCriterion())
     894        point->value += 1;
     895    }
     896  }
     897};
     898
    1016899
    1017900/** Checks whether each BoundaryLineSet in the Tesselation has two triangles.

  • src/tesselationhelpers.hpp

    r51a5c8 rf0f1cc  
    4343/********************************************** definitions *********************************/
    4444
    45 #define HULLEPSILON 1e-9 //!< TODO: Get rid of HULLEPSILON, points to numerical instabilities
     45#define HULLEPSILON 1e-10
    4646
    4747/********************************************** declarations *******************************/
    … …  
    5555bool existsIntersection(const Vector &point1, const Vector &point2, const Vector &point3, const Vector &point4);
    5656double CalculateVolumeofGeneralTetraeder(const Vector &a, const Vector &b, const Vector &c, const Vector &d);
    57 double CalculateAreaofGeneralTriangle(const Vector &A, const Vector &B, const Vector &C);
    5857double GetAngle(const Vector &point, const Vector &reference, const Vector &OrthogonalVector);
    5958
    … …  
    6968void WriteVrmlFile(ofstream * const vrmlfile, const Tesselation * const Tess, const PointCloud * const cloud);
    7069void CalculateConcavityPerBoundaryPoint(const Tesselation * const TesselStruct);
    71 void CalculateConstrictionPerBoundaryPoint(const Tesselation * const TesselStruct, const Tesselation * const Convex);
    7270double DistanceToTrianglePlane(const Vector *x, const BoundaryTriangleSet * const triangle);
    7371

  • src/unittests/CountBondsUnitTest.cpp

    r51a5c8 rf0f1cc  
    154154  Translator  = Vector(3,0,0);
    155155  TestMolecule2->Translate(&Translator);
    156   CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
    157   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, oxygen, NULL) );
     156  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL) );
     157  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, oxygen) );
    158158  //OutputTestMolecule(TestMolecule2, "testmolecule2-1.xyz");
    159159  Translator = Vector(-3,0,0);
    … …  
    163163  Translator = Vector(0,3,0);
    164164  TestMolecule2->Translate(&Translator);
    165   CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
     165  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL) );
    166166  //OutputTestMolecule(TestMolecule2, "testmolecule2-2.xyz");
    167167  Translator = Vector(0,-3,0);
    … …  
    172172  TestMolecule2->Scale((const double ** const)&mirror);
    173173  TestMolecule2->Translate(&Translator);
    174   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
     174  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
    175175  //OutputTestMolecule(TestMolecule2, "testmolecule2-3.xyz");
    176176  Translator = Vector(0,3,0);
    … …  
    181181  Translator = Vector(2,1,0);
    182182  TestMolecule2->Translate(&Translator);
    183   CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
     183  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL) );
    184184  //OutputTestMolecule(TestMolecule2, "testmolecule2-4.xyz");
    185185  Translator = Vector(-2,-1,0);
    … …  
    189189  Translator = Vector(0,0,3);
    190190  TestMolecule2->Translate(&Translator);
    191   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
     191  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
    192192  //OutputTestMolecule(TestMolecule2, "testmolecule2-5.xyz");
    193193  Translator = Vector(0,0,-3);
    … …  
    198198  TestMolecule2->Scale((const double ** const)&mirror);
    199199  TestMolecule2->Translate(&Translator);
    200   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
     200  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
    201201  //OutputTestMolecule(TestMolecule2, "testmolecule2-6.xyz");
    202202  Translator = Vector(3,0,0);
    … …  
    208208  TestMolecule2->Scale((const double ** const)&mirror);
    209209  TestMolecule2->Translate(&Translator);
    210   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
     210  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
    211211  //OutputTestMolecule(TestMolecule2, "testmolecule2-7.xyz");
    212212  Translator = Vector(-3,0,0);
    … …  
    219219  TestMolecule2->Translate(&Translator);
    220220  //OutputTestMolecule(TestMolecule2, "testmolecule2-8.xyz");
    221   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
     221  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
    222222  Translator = Vector(0,-3,0);
    223223  TestMolecule2->Translate(&Translator);

  • src/unittests/TestRunnerMain.cpp

    r51a5c8 rf0f1cc  
    1717#include "../../../TestRunnerClient.h"
    1818#include "../../../TestRunnerClient.cpp"
     19#else
     20#include "UnitTestMain.cpp"
     21#endif
    1922
    20 #else
    21 
    22 #include "unittests/UnitTestMain.cpp"
    23 
    24 #endif /* HAVE_ECUT */

  • src/unittests/UnitTestMain.cpp

    r51a5c8 rf0f1cc  
    66 */
    77
     8#include <cppunit/CompilerOutputter.h>
     9#include <cppunit/extensions/TestFactoryRegistry.h>
     10#include <cppunit/ui/text/TestRunner.h>
     11
    812// include config.h
    913#ifdef HAVE_CONFIG_H
    1014#include <config.h>
    1115#endif
    12 
    13 #include <cppunit/CompilerOutputter.h>
    14 #include <cppunit/extensions/TestFactoryRegistry.h>
    15 #include <cppunit/ui/text/TestRunner.h>
    1616
    1717/********************************************** Main routine **************************************/
    … …  
    3535  return wasSucessful ? 0 : 1;
    3636};
    37 

  • tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=23, E=64, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 -7.27e-07 -1.22006 0.930455 18.7229
    5 -7.27e-07 -1.22006 -0.849545 18.7229
    6 -1.2492 0.921941 0.930455 18.7227
    7 -1.2492 0.921941 -0.849545 18.7227
    8 1.2492 0.921941 -0.849545 18.7222
    9 1.2492 0.921941 0.930455 27.0641
    10 -2.4985 -1.22006 -0.849545 19.9769
    11 -2.4985 -1.22006 0.930455 27.4727
    12 2.4985 -1.22006 0.930455 19.9769
    13 2.4985 -1.22006 -0.849545 27.4727
    14 -4.6377 -0.336759 0.0404545 21.541
    15 -3.7477 0.921941 0.930455 18.8853
    16 -3.7477 0.921941 -0.849545 18.8853
    17 4.6377 -0.336759 0.0404545 10.6618
    18 3.7477 0.921941 -0.849545 18.5406
    19 3.7477 0.921941 0.930455 12.1988
    20 -7.27e-07 -0.590759 0.0404545 23.0174
    21 -1.2492 0.292641 0.0404545 23.0167
    22 1.2492 0.292641 0.0404545 20.1632
    23 -2.4985 -0.590759 0.0404545 18.9798
    24 2.4985 -0.590759 0.0404545 18.9798
    25 -3.7477 0.292641 0.0404545 39.5267
    26 3.7477 0.292641 0.0404545 23.2512
     4-7.27e-07 -1.22006 0.930455 3
     5-7.27e-07 -1.22006 -0.849545 3
     6-1.2492 0.921941 0.930455 3
     7-1.2492 0.921941 -0.849545 3
     81.2492 0.921941 -0.849545 3
     91.2492 0.921941 0.930455 3
     10-2.4985 -1.22006 -0.849545 4
     11-2.4985 -1.22006 0.930455 4
     122.4985 -1.22006 0.930455 4
     132.4985 -1.22006 -0.849545 4
     14-4.6377 -0.336759 0.0404545 6
     15-3.7477 0.921941 0.930455 5
     16-3.7477 0.921941 -0.849545 5
     174.6377 -0.336759 0.0404545 4
     183.7477 0.921941 -0.849545 4
     193.7477 0.921941 0.930455 4
     20-7.27e-07 -0.590759 0.0404545 6
     21-1.2492 0.292641 0.0404545 6
     221.2492 0.292641 0.0404545 6
     23-2.4985 -0.590759 0.0404545 6
     242.4985 -0.590759 0.0404545 6
     25-3.7477 0.292641 0.0404545 12
     263.7477 0.292641 0.0404545 12
    2727
    282814 15 23
    … …  
    38385 18 19
    39394 5 18
    40 6 18 19
    41 3 6 18
    42403 4 18
    43413 4 18
     423 18 19
     433 6 19
    44444 18 22
    45454 13 22
    … …  
    484812 13 22
    494912 13 22
    50 6 19 23
    51 6 16 23
     5016 19 23
     516 16 19
     5214 16 23
     5314 16 23
     549 14 23
     559 16 23
    525611 13 22
    535711 13 22
    … …  
    58628 11 22
    59638 12 22
    60 14 16 23
    61 14 16 23
    62 9 14 23
    63 9 16 23
     644 7 13
     652 4 7
     662 4 5
     672 5 10
     685 10 15
    64693 8 12
    65701 3 8
    … …  
    67721 6 9
    68736 9 16
    69 4 7 13
    70 2 4 7
    71 2 4 5
    72 2 5 10
    73 5 10 15
    747410 14 21
    75759 10 21
    … …  
    84842 17 20
    85852 7 20
     861 17 20
     871 8 20
    86887 8 20
    87897 8 20
    88907 11 20
    89918 11 20
    90 8 17 20
    91 1 8 17

  • tests/Tesselations/heptan/2.5/NonConvexEnvelope-heptan.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 -7.27e-07 -1.22006 0.930455 -17.4952
    5 -7.27e-07 -1.22006 -0.849545 -17.4952
    6 -1.2492 0.921941 0.930455 -19.6818
    7 -1.2492 0.921941 -0.849545 -15.323
    8 1.2492 0.921941 -0.849545 -17.495
    9 1.2492 0.921941 0.930455 -17.4951
    10 -2.4985 -1.22006 -0.849545 -13.1263
    11 -2.4985 -1.22006 0.930455 -10.8961
    12 2.4985 -1.22006 0.930455 -13.1263
    13 2.4985 -1.22006 -0.849545 -10.8961
    14 -4.6377 -0.336759 0.0404545 -9.35471
    15 -3.7477 0.921941 0.930455 -9.24444
    16 -3.7477 0.921941 -0.849545 -11.4805
    17 4.6377 -0.336759 0.0404545 -9.35473
    18 3.7477 0.921941 -0.849545 -11.4805
    19 3.7477 0.921941 0.930455 -9.24445
     4-7.27e-07 -1.22006 0.930455 0
     5-7.27e-07 -1.22006 -0.849545 0
     6-1.2492 0.921941 0.930455 0
     7-1.2492 0.921941 -0.849545 0
     81.2492 0.921941 -0.849545 0
     91.2492 0.921941 0.930455 0
     10-2.4985 -1.22006 -0.849545 0
     11-2.4985 -1.22006 0.930455 0
     122.4985 -1.22006 0.930455 0
     132.4985 -1.22006 -0.849545 0
     14-4.6377 -0.336759 0.0404545 0
     15-3.7477 0.921941 0.930455 0
     16-3.7477 0.921941 -0.849545 0
     174.6377 -0.336759 0.0404545 0
     183.7477 0.921941 -0.849545 0
     193.7477 0.921941 0.930455 0
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 7 11 13
    30 4 7 13
    31 2 4 7
    32 2 4 5
    33 2 5 10
    34 5 10 15
    35 10 14 15
     298 11 12
     303 8 12
     311 3 8
     321 3 6
     331 6 9
     346 9 16
     359 14 16
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 9 14 16
    43 6 9 16
    44 1 6 9
    45 1 3 6
    46 1 3 8
    47 3 8 12
    48 8 11 12
     4210 14 15
     435 10 15
     442 5 10
     452 4 5
     462 4 7
     474 7 13
     487 11 13

  • tests/Tesselations/heptan/2/NonConvexEnvelope-heptan.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 -7.27e-07 -1.22006 0.930455 -17.4952
    5 -7.27e-07 -1.22006 -0.849545 -17.4952
    6 -1.2492 0.921941 0.930455 -19.6818
    7 -1.2492 0.921941 -0.849545 -15.323
    8 1.2492 0.921941 -0.849545 -17.495
    9 1.2492 0.921941 0.930455 -17.4951
    10 -2.4985 -1.22006 -0.849545 -13.1263
    11 -2.4985 -1.22006 0.930455 -10.8961
    12 2.4985 -1.22006 0.930455 -13.1263
    13 2.4985 -1.22006 -0.849545 -10.8961
    14 -4.6377 -0.336759 0.0404545 -9.35471
    15 -3.7477 0.921941 0.930455 -9.24444
    16 -3.7477 0.921941 -0.849545 -11.4805
    17 4.6377 -0.336759 0.0404545 -9.35473
    18 3.7477 0.921941 -0.849545 -11.4805
    19 3.7477 0.921941 0.930455 -9.24445
     4-7.27e-07 -1.22006 0.930455 0
     5-7.27e-07 -1.22006 -0.849545 0
     6-1.2492 0.921941 0.930455 0
     7-1.2492 0.921941 -0.849545 0
     81.2492 0.921941 -0.849545 0
     91.2492 0.921941 0.930455 0
     10-2.4985 -1.22006 -0.849545 0
     11-2.4985 -1.22006 0.930455 0
     122.4985 -1.22006 0.930455 0
     132.4985 -1.22006 -0.849545 0
     14-4.6377 -0.336759 0.0404545 0
     15-3.7477 0.921941 0.930455 0
     16-3.7477 0.921941 -0.849545 0
     174.6377 -0.336759 0.0404545 0
     183.7477 0.921941 -0.849545 0
     193.7477 0.921941 0.930455 0
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 7 11 13
    30 4 7 13
    31 2 4 7
    32 2 4 5
    33 2 5 10
    34 5 10 15
    35 10 14 15
     298 11 12
     303 8 12
     311 3 8
     321 3 6
     331 6 9
     346 9 16
     359 14 16
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 9 14 16
    43 6 9 16
    44 1 6 9
    45 1 3 6
    46 1 3 8
    47 3 8 12
    48 8 11 12
     4210 14 15
     435 10 15
     442 5 10
     452 4 5
     462 4 7
     474 7 13
     487 11 13

  • tests/Tesselations/heptan/25/NonConvexEnvelope-heptan.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 -7.27e-07 -1.22006 0.930455 -17.4952
    5 -7.27e-07 -1.22006 -0.849545 -17.4952
    6 -1.2492 0.921941 0.930455 -19.6818
    7 -1.2492 0.921941 -0.849545 -15.323
    8 1.2492 0.921941 -0.849545 -17.495
    9 1.2492 0.921941 0.930455 -17.4951
    10 -2.4985 -1.22006 -0.849545 -13.1263
    11 -2.4985 -1.22006 0.930455 -10.8961
    12 2.4985 -1.22006 0.930455 -13.1263
    13 2.4985 -1.22006 -0.849545 -10.8961
    14 -4.6377 -0.336759 0.0404545 -9.35471
    15 -3.7477 0.921941 0.930455 -9.24444
    16 -3.7477 0.921941 -0.849545 -11.4805
    17 4.6377 -0.336759 0.0404545 -9.35473
    18 3.7477 0.921941 -0.849545 -11.4805
    19 3.7477 0.921941 0.930455 -9.24445
     4-7.27e-07 -1.22006 0.930455 0
     5-7.27e-07 -1.22006 -0.849545 0
     6-1.2492 0.921941 0.930455 0
     7-1.2492 0.921941 -0.849545 0
     81.2492 0.921941 -0.849545 0
     91.2492 0.921941 0.930455 0
     10-2.4985 -1.22006 -0.849545 0
     11-2.4985 -1.22006 0.930455 0
     122.4985 -1.22006 0.930455 0
     132.4985 -1.22006 -0.849545 0
     14-4.6377 -0.336759 0.0404545 0
     15-3.7477 0.921941 0.930455 0
     16-3.7477 0.921941 -0.849545 0
     174.6377 -0.336759 0.0404545 0
     183.7477 0.921941 -0.849545 0
     193.7477 0.921941 0.930455 0
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 7 11 13
    30 4 7 13
    31 2 4 7
    32 2 4 5
    33 2 5 10
    34 5 10 15
    35 10 14 15
     298 11 12
     303 8 12
     311 3 8
     321 3 6
     331 6 9
     346 9 16
     359 14 16
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 9 14 16
    43 6 9 16
    44 1 6 9
    45 1 3 6
    46 1 3 8
    47 3 8 12
    48 8 11 12
     4210 14 15
     435 10 15
     442 5 10
     452 4 5
     462 4 7
     474 7 13
     487 11 13

  • tests/Tesselations/heptan/3.5/NonConvexEnvelope-heptan.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 -7.27e-07 -1.22006 0.930455 -17.4952
    5 -7.27e-07 -1.22006 -0.849545 -17.4952
    6 -1.2492 0.921941 0.930455 -19.6818
    7 -1.2492 0.921941 -0.849545 -15.323
    8 1.2492 0.921941 -0.849545 -17.495
    9 1.2492 0.921941 0.930455 -17.4951
    10 -2.4985 -1.22006 -0.849545 -13.1263
    11 -2.4985 -1.22006 0.930455 -10.8961
    12 2.4985 -1.22006 0.930455 -13.1263
    13 2.4985 -1.22006 -0.849545 -10.8961
    14 -4.6377 -0.336759 0.0404545 -9.35471
    15 -3.7477 0.921941 0.930455 -9.24444
    16 -3.7477 0.921941 -0.849545 -11.4805
    17 4.6377 -0.336759 0.0404545 -9.35473
    18 3.7477 0.921941 -0.849545 -11.4805
    19 3.7477 0.921941 0.930455 -9.24445
     4-7.27e-07 -1.22006 0.930455 0
     5-7.27e-07 -1.22006 -0.849545 0
     6-1.2492 0.921941 0.930455 0
     7-1.2492 0.921941 -0.849545 0
     81.2492 0.921941 -0.849545 0
     91.2492 0.921941 0.930455 0
     10-2.4985 -1.22006 -0.849545 0
     11-2.4985 -1.22006 0.930455 0
     122.4985 -1.22006 0.930455 0
     132.4985 -1.22006 -0.849545 0
     14-4.6377 -0.336759 0.0404545 0
     15-3.7477 0.921941 0.930455 0
     16-3.7477 0.921941 -0.849545 0
     174.6377 -0.336759 0.0404545 0
     183.7477 0.921941 -0.849545 0
     193.7477 0.921941 0.930455 0
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 7 11 13
    30 4 7 13
    31 2 4 7
    32 2 4 5
    33 2 5 10
    34 5 10 15
    35 10 14 15
     298 11 12
     303 8 12
     311 3 8
     321 3 6
     331 6 9
     346 9 16
     359 14 16
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 9 14 16
    43 6 9 16
    44 1 6 9
    45 1 3 6
    46 1 3 8
    47 3 8 12
    48 8 11 12
     4210 14 15
     435 10 15
     442 5 10
     452 4 5
     462 4 7
     474 7 13
     487 11 13

  • tests/Tesselations/heptan/3/NonConvexEnvelope-heptan.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 -7.27e-07 -1.22006 0.930455 -17.4952
    5 -7.27e-07 -1.22006 -0.849545 -17.4952
    6 -1.2492 0.921941 0.930455 -19.6818
    7 -1.2492 0.921941 -0.849545 -15.323
    8 1.2492 0.921941 -0.849545 -17.495
    9 1.2492 0.921941 0.930455 -17.4951
    10 -2.4985 -1.22006 -0.849545 -13.1263
    11 -2.4985 -1.22006 0.930455 -10.8961
    12 2.4985 -1.22006 0.930455 -13.1263
    13 2.4985 -1.22006 -0.849545 -10.8961
    14 -4.6377 -0.336759 0.0404545 -9.35471
    15 -3.7477 0.921941 0.930455 -9.24444
    16 -3.7477 0.921941 -0.849545 -11.4805
    17 4.6377 -0.336759 0.0404545 -9.35473
    18 3.7477 0.921941 -0.849545 -11.4805
    19 3.7477 0.921941 0.930455 -9.24445
     4-7.27e-07 -1.22006 0.930455 0
     5-7.27e-07 -1.22006 -0.849545 0
     6-1.2492 0.921941 0.930455 0
     7-1.2492 0.921941 -0.849545 0
     81.2492 0.921941 -0.849545 0
     91.2492 0.921941 0.930455 0
     10-2.4985 -1.22006 -0.849545 0
     11-2.4985 -1.22006 0.930455 0
     122.4985 -1.22006 0.930455 0
     132.4985 -1.22006 -0.849545 0
     14-4.6377 -0.336759 0.0404545 0
     15-3.7477 0.921941 0.930455 0
     16-3.7477 0.921941 -0.849545 0
     174.6377 -0.336759 0.0404545 0
     183.7477 0.921941 -0.849545 0
     193.7477 0.921941 0.930455 0
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 7 11 13
    30 4 7 13
    31 2 4 7
    32 2 4 5
    33 2 5 10
    34 5 10 15
    35 10 14 15
     298 11 12
     303 8 12
     311 3 8
     321 3 6
     331 6 9
     346 9 16
     359 14 16
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 9 14 16
    43 6 9 16
    44 1 6 9
    45 1 3 6
    46 1 3 8
    47 3 8 12
    48 8 11 12
     4210 14 15
     435 10 15
     442 5 10
     452 4 5
     462 4 7
     474 7 13
     487 11 13

  • tests/Tesselations/heptan/4/NonConvexEnvelope-heptan.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 -7.27e-07 -1.22006 0.930455 -17.4952
    5 -7.27e-07 -1.22006 -0.849545 -17.4952
    6 -1.2492 0.921941 0.930455 -19.6818
    7 -1.2492 0.921941 -0.849545 -15.323
    8 1.2492 0.921941 -0.849545 -17.495
    9 1.2492 0.921941 0.930455 -17.4951
    10 -2.4985 -1.22006 -0.849545 -13.1263
    11 -2.4985 -1.22006 0.930455 -10.8961
    12 2.4985 -1.22006 0.930455 -13.1263
    13 2.4985 -1.22006 -0.849545 -10.8961
    14 -4.6377 -0.336759 0.0404545 -9.35471
    15 -3.7477 0.921941 0.930455 -9.24444
    16 -3.7477 0.921941 -0.849545 -11.4805
    17 4.6377 -0.336759 0.0404545 -9.35473
    18 3.7477 0.921941 -0.849545 -11.4805
    19 3.7477 0.921941 0.930455 -9.24445
     4-7.27e-07 -1.22006 0.930455 0
     5-7.27e-07 -1.22006 -0.849545 0
     6-1.2492 0.921941 0.930455 0
     7-1.2492 0.921941 -0.849545 0
     81.2492 0.921941 -0.849545 0
     91.2492 0.921941 0.930455 0
     10-2.4985 -1.22006 -0.849545 0
     11-2.4985 -1.22006 0.930455 0
     122.4985 -1.22006 0.930455 0
     132.4985 -1.22006 -0.849545 0
     14-4.6377 -0.336759 0.0404545 0
     15-3.7477 0.921941 0.930455 0
     16-3.7477 0.921941 -0.849545 0
     174.6377 -0.336759 0.0404545 0
     183.7477 0.921941 -0.849545 0
     193.7477 0.921941 0.930455 0
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 7 11 13
    30 4 7 13
    31 2 4 7
    32 2 4 5
    33 2 5 10
    34 5 10 15
    35 10 14 15
     298 11 12
     303 8 12
     311 3 8
     321 3 6
     331 6 9
     346 9 16
     359 14 16
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 9 14 16
    43 6 9 16
    44 1 6 9
    45 1 3 6
    46 1 3 8
    47 3 8 12
    48 8 11 12
     4210 14 15
     435 10 15
     442 5 10
     452 4 5
     462 4 7
     474 7 13
     487 11 13

  • tests/regression/Tesselation/1/post/NonConvexEnvelope.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="test", N=8, E=12, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 9.78209 2.64589 2.64589 -9.24443
    5 9.78209 2.64589 4.42589 -11.4804
    6 10.672 3.90454 3.53589 -9.35464
    7 8.53279 4.78789 2.64589 -9.11459
    8 8.53279 4.78789 4.42589 -9.11459
    9 6.39363 3.90454 3.53589 -9.35431
    10 7.28359 2.64589 2.64589 -11.4803
    11 7.28359 2.64589 4.42589 -9.24433
     49.78209 2.64589 2.64589 0
     59.78209 2.64589 4.42589 0
     610.672 3.90454 3.53589 0
     78.53279 4.78789 2.64589 0
     88.53279 4.78789 4.42589 0
     96.39363 3.90454 3.53589 0
     107.28359 2.64589 2.64589 0
     117.28359 2.64589 4.42589 0
    1212
    13131 3 4

  • tests/regression/Tesselation/2/post/ConvexEnvelope.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="test", N=8, E=12, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 9.78209 2.64589 2.64589 -9.24443
    5 9.78209 2.64589 4.42589 -11.4804
    6 10.672 3.90454 3.53589 -9.35464
    7 8.53279 4.78789 2.64589 -9.11459
    8 8.53279 4.78789 4.42589 -9.11459
    9 6.39363 3.90454 3.53589 -9.35431
    10 7.28359 2.64589 2.64589 -11.4803
    11 7.28359 2.64589 4.42589 -9.24433
     49.78209 2.64589 2.64589 0
     59.78209 2.64589 4.42589 0
     610.672 3.90454 3.53589 0
     78.53279 4.78789 2.64589 0
     88.53279 4.78789 4.42589 0
     96.39363 3.90454 3.53589 0
     107.28359 2.64589 2.64589 0
     117.28359 2.64589 4.42589 0
    1212
    13131 3 4

  • tests/regression/Tesselation/2/post/NonConvexEnvelope.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="test", N=8, E=12, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 9.78209 2.64589 2.64589 -9.24443
    5 9.78209 2.64589 4.42589 -11.4804
    6 10.672 3.90454 3.53589 -9.35464
    7 8.53279 4.78789 2.64589 -9.11459
    8 8.53279 4.78789 4.42589 -9.11459
    9 6.39363 3.90454 3.53589 -9.35431
    10 7.28359 2.64589 2.64589 -11.4803
    11 7.28359 2.64589 4.42589 -9.24433
     49.78209 2.64589 2.64589 0
     59.78209 2.64589 4.42589 0
     610.672 3.90454 3.53589 0
     78.53279 4.78789 2.64589 0
     88.53279 4.78789 4.42589 0
     96.39363 3.90454 3.53589 0
     107.28359 2.64589 2.64589 0
     117.28359 2.64589 4.42589 0
    1212
    13131 3 4

  • tests/regression/Tesselation/3/post/NonConvexEnvelope.dat

    r51a5c8 rf0f1cc  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="test", N=44, E=86, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 6.9077 1.1106 0.1214 -6.99715
    5 0.3612 -3.628 1.323 6.00416
    6 0.4884 -3.5983 -0.4521 11.8428
    7 1.4985 -2.5112 0.5308 6.07951
    8 -1.9534 -3.5752 0.5362 -4.26914
    9 -1.1883 -0.199 1.5176 14.2992
    10 -0.7165 -1.6046 2.5129 6.2134
    11 1.7627 -1.4479 -0.8349 7.15053
    12 -1.003 -1.3584 -2.8848 32.043
    13 0.0217 -2.6629 -2.2008 16.8009
    14 -2.8885 -1.5706 1.7543 -1.77076
    15 -2.0579 -3.6765 -1.7622 -7.05319
    16 -2.9259 -2.1146 -1.7672 33.6663
    17 1.0353 0.1785 2.542 48.8869
    18 1.6325 -1.3323 1.8306 1.44108
    19 0.7271 1.177 0.3594 27.9872
    20 1.3374 -0.2942 -2.961 13.6459
    21 0.6036 1.0859 -2.1126 98.521
    22 -3.2034 -0.5041 -1.0881 8.44805
    23 -5.1809 -1.8679 0.9687 -6.07448
    24 -4.6025 -2.4721 -0.6025 -6.52057
    25 -4.3385 -3.4329 0.8725 -4.12716
    26 3.191 1.3217 -2.8354 -10.5968
    27 -4.0905 0.6312 1.6028 21.8745
    28 2.8131 1.4776 2.5103 -0.774194
    29 3.9137 2.2936 1.3739 -2.51806
    30 2.159 2.5738 1.2698 151.494
    31 3.6606 -0.4593 2.1396 2.60004
    32 3.2007 -1.4419 0.7311 2.29272
    33 -3.3002 2.3589 0.0094 461.065
    34 -4.377 1.6962 -1.2433 43.4649
    35 5.2593 1.4547 -1.7445 -6.26082
    36 4.6863 2.7674 -0.6775 -8.55931
    37 5.746 -0.9031 1.204 -1.29544
    38 5.1212 -0.8867 -0.4582 31.5177
    39 -5.2641 2.8314 1.4476 21.5516
    40 5.2727 1.6068 1.2828 -2.57271
    41 -6.2394 4.6427 0.0632 -9.24392
    42 -4.4738 4.5591 -0.1458 62.5211
    43 -5.5506 3.8964 -1.3985 -10.3613
    44 -6.7081 0.9923 0.6224 -7.08885
    45 -7.5442 2.5597 0.5118 -11.4252
    46 -6.8554 1.8134 -0.9499 3.80444
    47 7.1391 2.0447 0.0264 -7.88713
     46.9077 1.1106 0.1214 1
     50.3612 -3.628 1.323 1
     60.4884 -3.5983 -0.4521 3
     71.4985 -2.5112 0.5308 4
     8-1.9534 -3.5752 0.5362 2
     9-1.1883 -0.199 1.5176 3
     10-0.7165 -1.6046 2.5129 1
     111.7627 -1.4479 -0.8349 4
     12-1.003 -1.3584 -2.8848 2
     130.0217 -2.6629 -2.2008 1
     14-2.8885 -1.5706 1.7543 2
     15-2.0579 -3.6765 -1.7622 0
     16-2.9259 -2.1146 -1.7672 1
     171.0353 0.1785 2.542 3
     181.6325 -1.3323 1.8306 2
     190.7271 1.177 0.3594 3
     201.3374 -0.2942 -2.961 2
     210.6036 1.0859 -2.1126 3
     22-3.2034 -0.5041 -1.0881 3
     23-5.1809 -1.8679 0.9687 1
     24-4.6025 -2.4721 -0.6025 2
     25-4.3385 -3.4329 0.8725 0
     263.191 1.3217 -2.8354 1
     27-4.0905 0.6312 1.6028 3
     282.8131 1.4776 2.5103 0
     293.9137 2.2936 1.3739 0
     302.159 2.5738 1.2698 5
     313.6606 -0.4593 2.1396 2
     323.2007 -1.4419 0.7311 4
     33-3.3002 2.3589 0.0094 8
     34-4.377 1.6962 -1.2433 3
     355.2593 1.4547 -1.7445 0
     364.6863 2.7674 -0.6775 0
     375.746 -0.9031 1.204 0
     385.1212 -0.8867 -0.4582 4
     39-5.2641 2.8314 1.4476 0
     405.2727 1.6068 1.2828 2
     41-6.2394 4.6427 0.0632 0
     42-4.4738 4.5591 -0.1458 3
     43-5.5506 3.8964 -1.3985 0
     44-6.7081 0.9923 0.6224 2
     45-7.5442 2.5597 0.5118 0
     46-6.8554 1.8134 -0.9499 1
     477.1391 2.0447 0.0264 0
    4848
    49491 32 44

  • tests/regression/testsuite-filling.at

    r51a5c8 rf0f1cc  
    1818AT_KEYWORDS([filling])
    1919AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/2/pre/test.conf .], 0)
    20 AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -u 1.3 --molecule-by-id 0], 0, [stdout], [stderr])
     20AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -u 1.3], 0, [stdout], [stderr])
    2121#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Filling/2/post/$file], 0, [ignore], [ignore])
    2222AT_CLEANUP

  • tests/regression/testsuite-molecules.at

    r51a5c8 rf0f1cc  
    6161AT_KEYWORDS([Molecules])
    6262AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/pre/test.* .], 0)
    63 AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -m 0], 0, [stdout], [stderr])
     63AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -m 1], 0, [stdout], [stderr])
    6464#AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/8/post/$file], 0, [ignore], [ignore])
    6565AT_CLEANUP
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