Changes in / [f0f1cc:51a5c8]


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20 added
43 edited

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  • configure.ac

    rf0f1cc r51a5c8  
    3333AX_BOOST_THREAD
    3434#AX_BOOST_SERIALIZATION
     35
     36#QT4 libraries
     37gw_CHECK_QT4
     38AX_CHECK_GLU
     39AC_MSG_NOTICE(["GLU_CFLAGS: $GLU_CFLAGS, GLU_CXXFLAGS: $GLU_CXXFLAGS, GLU_LDFLAGS: $GLU_LDFLAGS, GLU_LIBS: $GLU_LIBS"])
     40
    3541
    3642# Checks for header files.

  • doc/class structure.uxf

    rf0f1cc r51a5c8  
    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>294</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>210</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>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
     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
    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>532</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>448</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>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
     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
    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>280</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>196</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>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
     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
    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>427</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>343</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>609</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>525</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>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
     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
    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>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
     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
    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>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
     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
    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>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
     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
    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>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
     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
    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>707</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>896</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>742</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>1330</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>623</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>812</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>658</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>1246</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>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
     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
    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>539</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>455</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>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;-
    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>980</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>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;-
     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>896</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>1064</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>980</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>1218</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>1134</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>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
     324BondsPerSPCount: 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
    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>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;-
    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>2282</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>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;-
     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>2198</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>266</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>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>
     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--
     334x: 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>

  • src/Actions/MapOfActions.cpp

    rf0f1cc r51a5c8  
    4242#include "Actions/MoleculeAction/FillWithMoleculeAction.hpp"
    4343#include "Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp"
     44#include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
    4445#include "Actions/MoleculeAction/SaveAdjacencyAction.hpp"
    4546#include "Actions/MoleculeAction/SaveBondsAction.hpp"
    4647#include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
     48#include "Actions/MoleculeAction/SuspendInWaterAction.hpp"
    4749#include "Actions/MoleculeAction/TranslateAction.hpp"
    4850#include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
    … …  
    288290
    289291  // 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
    290301  MenuContainsActionMap.insert( pair<std::string, std::string> ("analysis", "molecular-volume") );
    291302  MenuContainsActionMap.insert( pair<std::string, std::string> ("analysis", "pair-correlation") );
    … …  
    445456  new MoleculeFillWithMoleculeAction();
    446457  new MoleculeLinearInterpolationofTrajectoriesAction();
     458  new MoleculeRotateToPrincipalAxisSystemAction();
    447459  new MoleculeSaveAdjacencyAction();
    448460  new MoleculeSaveBondsAction();
    449461  new MoleculeSaveTemperatureAction();
     462  new MoleculeSuspendInWaterAction();
    450463  new MoleculeTranslateAction();
    451464  new MoleculeVerletIntegrationAction();

  • src/Actions/MapOfActions.hpp

    rf0f1cc r51a5c8  
    145145
    146146  std::multimap <std::string, std::string> MenuContainsActionMap;
     147  std::map <std::string, std::pair<std::string,std::string> > MenuDescription;
    147148
    148149  // instantiates and puts all known actions into the ActionRegistry

  • src/Actions/MoleculeAction/SuspendInWaterAction.cpp

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

  • src/Actions/Process.cpp

    rf0f1cc r51a5c8  
    4141
    4242int Process::getCurrStep(){
    43   OBSERVE;
    4443  return currStep;
    4544}
    4645
    4746void Process::setCurrStep(int _currStep){
     47  OBSERVE;
    4848  currStep = _currStep;
    4949}
    … …  
    5555    return 0;
    5656}
    57 
    5857int Process::getMaxSteps(){
    5958  return maxSteps;

  • src/Actions/TesselationAction/ConvexEnvelopeAction.hpp

    rf0f1cc r51a5c8  
    3131};
    3232
    33 
    3433#endif // CONVEXENVELOPEACTION_HPP

  • src/Legacy/oldmenu.cpp

    rf0f1cc r51a5c8  
    1010
    1111#include "Legacy/oldmenu.hpp"
     12#include "analysis_bonds.hpp"
    1213#include "analysis_correlation.hpp"
    1314#include "World.hpp"
    … …  
    509510  Log() << Verbose(0) << " f - calculate temperature from current velocity" << endl;
    510511  Log() << Verbose(0) << " g - output all temperatures per step from velocities" << endl;
     512  Log() << Verbose(0) << " h - count the number of hydrogen bonds" << endl;
    511513  Log() << Verbose(0) << "all else - go back" << endl;
    512514  Log() << Verbose(0) << "===============================================" << endl;
    … …  
    597599        output->close();
    598600        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;
    599614      }
    600615      break;

  • src/Makefile.am

    rf0f1cc r51a5c8  
    102102  Patterns/Singleton.hpp
    103103
     104QTUIMOC_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 
     112QTUIMOC_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
    104120DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
    105121  Descriptors/AtomIdDescriptor.cpp \
    … …  
    130146                                  Exceptions/SkewException.hpp \
    131147                                  Exceptions/ZeroVectorException.hpp
     148                                 
     149QTUISOURCE = ${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             
     159QTUIHEADER = ${QTUIMOC_HEADER} UIElements/QT4/QTUIFactory.hpp
     160
     161QTUI_DEFS =
    132162
    133163SOURCE = \
    … …  
    227257
    228258BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
     259GUI_LIBS = ${QT_LDADD} ${QT_LIB_GUI} -lQtOpenGL ${GLU_LIBS}
    229260INCLUDES = -I$(top_srcdir)/src/unittests -I$(top_srcdir)/src/Actions -I$(top_srcdir)/src/UIElements
    230261
    231 noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a libparser.a
    232 bin_PROGRAMS = molecuilder joiner analyzer
     262noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a libmenu.a libparser.a
     263bin_PROGRAMS = molecuilder molecuildergui joiner analyzer
     264
    233265molecuilderdir = ${bindir}
     266
    234267libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
     268
     269libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER}
    235270libparser_a_SOURCES = ${PARSERSOURCE} ${PARSERHEADER}
    236271libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
     272
    237273molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
    238 molecuilder_LDFLAGS = $(BOOST_LDFLAGS)
    239 molecuilder_SOURCES = builder.cpp
    240 molecuilder_LDADD =  UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilder.a libparser.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
     274
     275molecuilder_CXXFLAGS = $(BOOST_CPPFLAGS)
     276#molecuilder_CXXFLAGS += -DNO_CACHING
     277molecuilder_LDFLAGS = $(BOOST_LIB)
     278molecuilder_SOURCES = ${LEGACYSOURCE} builder.cpp
     279molecuilder_SOURCES += $(srcdir)/version.c
     280molecuilder_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
     283molecuildergui_SOURCES = ${QTUISOURCE} ${LEGACYSOURCE} builder.cpp
     284molecuildergui_SOURCES += $(srcdir)/version.c
     285molecuildergui_CXXFLAGS = ${QT_CXXFLAGS} ${GLU_CXXFLAGS} -DUSE_GUI_QT
     286molecuildergui_LDFLAGS = $(BOOST_LIB) ${QT_LDFLAGS} ${GLU_LDFLAGS}
     287molecuildergui_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
    241289joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
    242290joiner_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
     291
    243292analyzer_SOURCES = analyzer.cpp datacreator.cpp parser.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp
    244293analyzer_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
     307MOSTLYCLEANFILES = ${QTUIMOC_TARGETS}
     308       
     309#EXTRA_DIST = ${molecuilder_DATA}
    245310
    246311FORCE:
    … …  
    258323        echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
    259324
    260 molecuilder_SOURCES += $(srcdir)/version.c
     325

  • src/UIElements/Dialog.cpp

    rf0f1cc r51a5c8  
    3434
    3535bool Dialog::display(){
     36  if(checkAll()){
     37    setAll();
     38    return true;
     39  }
     40  else{
     41    return false;
     42  }
     43}
     44
     45bool Dialog::checkAll(){
    3646  list<Query*>::iterator iter;
    3747  bool retval = true;
    … …  
    4454    }
    4555  }
    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   }
    5256  return retval;
     57}
     58
     59void Dialog::setAll(){
     60  list<Query*>::iterator iter;
     61  for(iter=queries.begin(); iter!=queries.end(); iter++) {
     62    (*iter)->setResult();
     63  }
    5364}
    5465

  • src/UIElements/Dialog.hpp

    rf0f1cc r51a5c8  
    3636
    3737  virtual bool display();
     38
     39  virtual bool checkAll();
     40  virtual void setAll();
    3841
    3942protected:

  • src/UIElements/MainWindow.cpp

    rf0f1cc r51a5c8  
    1111
    1212MainWindow::MainWindow()
    13 {
    14   // TODO Auto-generated constructor stub
    15 
    16 }
     13{}
    1714
    1815MainWindow::~MainWindow()
    19 {
    20   // TODO Auto-generated destructor stub
    21 }
     16{}

  • src/UIElements/TextUI/TextUIFactory.cpp

    rf0f1cc r51a5c8  
    99#include "UIElements/TextUI/TextWindow.hpp"
    1010#include "UIElements/TextUI/TextDialog.hpp"
    11 
    1211
    1312TextUIFactory::TextUIFactory()

  • src/UIElements/TextUI/TextUIFactory.hpp

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

  • src/UIElements/TextUI/TextWindow.cpp

    rf0f1cc r51a5c8  
    2525#include "Views/StreamStringView.hpp"
    2626#include "Views/MethodStringView.hpp"
     27#include "Helpers/MemDebug.hpp"
    2728
    2829#include "defs.hpp"
    … …  
    7071  new ActionMenuItem('a',"set molecule (in)active",main_menu,setMoleculeAction);
    7172
    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);
     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  }
    10380
    10481  new SeperatorItem(main_menu);

  • src/UIElements/UIFactory.cpp

    rf0f1cc r51a5c8  
    1212#include "UIElements/UIFactory.hpp"
    1313#include "Helpers/Assert.hpp"
     14#include "Helpers/MemDebug.hpp"
    1415
    1516using namespace std;

  • src/UIElements/UIFactory.hpp

    rf0f1cc r51a5c8  
    3030  friend class Singleton<UIFactory,false>;
    3131public:
     32
    3233  /**
    3334   * Produce some kind of main window, of whichever type was chosen when the factory was created

  • src/analysis_bonds.cpp

    rf0f1cc r51a5c8  
    121121 * \param *molecules molecules to count bonds
    122122 * \param *InterfaceElement or NULL
    123  */
    124 int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL)
     123 * \param *Interface2Element or NULL
     124 */
     125int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL, const element * Interface2Element = NULL)
    125126{
    126127  int count = 0;
    … …  
    128129  double Otherangle = 0.;
    129130  bool InterfaceFlag = false;
     131  bool Interface2Flag = false;
    130132  bool OtherHydrogenFlag = true;
    131133  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); ++MolWalker) {
    … …  
    145147              OtherHydrogens = 0;
    146148              InterfaceFlag = (InterfaceElement == NULL);
     149              Interface2Flag = (Interface2Element == NULL);
    147150              for (BondList::const_iterator BondRunner = (*Runner)->ListOfBonds.begin(); BondRunner != (*Runner)->ListOfBonds.end(); BondRunner++) {
    148151                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Runner);
    … …  
    155158                }
    156159                InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
     160                Interface2Flag = Interface2Flag || (OtherAtom->type == Interface2Element);
    157161              }
    158162              DoLog(1) && (Log() << Verbose(1) << "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens." << endl);
    … …  
    168172                  break;
    169173              }
    170               if (InterfaceFlag && OtherHydrogenFlag) {
     174              if (InterfaceFlag && Interface2Flag && OtherHydrogenFlag) {
    171175                // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
    172176                for (BondList::const_iterator BondRunner = (*Walker)->ListOfBonds.begin(); BondRunner != (*Walker)->ListOfBonds.end(); BondRunner++) {

  • src/analysis_bonds.hpp

    rf0f1cc r51a5c8  
    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);
     35int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, const element * InterfaceElement, const element * Interface2Element);
    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

    rf0f1cc r51a5c8  
    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

    rf0f1cc r51a5c8  
    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"
    6275#include "verbose.hpp"
    6376#include "World.hpp"
    … …  
    146159      UIFactory::makeUserInterface("CommandLine");
    147160    } else {
    148       DoLog(0) && (Log() << Verbose(0) << "Setting UI to Text." << endl);
    149       UIFactory::registerFactory(new TextUIFactory::description());
    150       UIFactory::makeUserInterface("Text");
     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
    151171    }
    152172  }

  • src/defs.hpp

    rf0f1cc r51a5c8  
    8282#define STD_SEPERATOR_SPACER '-'
    8383
     84#define MOLECUILDER_NAME "Molecuilder"
     85
    8486#endif /*DEFS_HPP_*/

  • src/molecule.hpp

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

  • src/tesselation.cpp

    rf0f1cc r51a5c8  
    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 */
     248double BoundaryLineSet::CalculateConvexity() const
     249{
     250  Info FunctionInfo(__func__);
    233251  Vector BaseLineCenter, BaseLineNormal, BaseLine, helper[2], NormalCheck;
    234252  // get the two triangles
    … …  
    279297  BaseLineNormal.Scale(-1.);
    280298  double angle = GetAngle(helper[0], helper[1], BaseLineNormal);
    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   }
     299  return (angle - M_PI);
    288300}
    289301
    … …  
    304316/** Returns other endpoint of the line.
    305317 * \param *point other endpoint
    306  * \return NULL - if endpoint not contained in BoundaryLineSet, or pointer to BoundaryPointSet otherwise
     318 * \return NULL - if endpoint not contained in BoundaryLineSet::lines, or pointer to BoundaryPointSet otherwise
    307319 */
    308320class BoundaryPointSet *BoundaryLineSet::GetOtherEndpoint(const BoundaryPointSet * const point) const
    … …  
    315327  else
    316328    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 */
     336class 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;
    317345}
    318346;
    … …  
    661689;
    662690
     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 */
     695class 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
    663709/** Calculates the center point of the triangle.
    664710 * Is third of the sum of all endpoints.
    … …  
    11101156    TesselPointList *ListofPoints = LC->GetPointsInsideSphere(RADIUS, (*VRunner));
    11111157
    1112     DoLog(1) && (Log() << Verbose(1) << "The following atoms are inside sphere at " << OtherOptCenter << ":" << endl);
     1158    DoLog(1) && (Log() << Verbose(1) << "The following atoms are inside sphere at " << (*VRunner) << ":" << endl);
    11131159    for (TesselPointList::const_iterator Runner = ListofPoints->begin(); Runner != ListofPoints->end(); ++Runner)
    1114       DoLog(1) && (Log() << Verbose(1) << "  " << *(*Runner) << " with distance " << (*Runner)->node->distance(OtherOptCenter) << "." << endl);
     1160      DoLog(1) && (Log() << Verbose(1) << "  " << *(*Runner) << " with distance " << (*Runner)->node->distance(*(*VRunner)) << "." << endl);
    11151161
    11161162    // remove baseline's endpoints and candidates
    … …  
    11281174      DoeLog(1) && (eLog() << Verbose(1) << "External atoms inside of sphere at " << *(*VRunner) << ":" << endl);
    11291175      for (TesselPointList::const_iterator Runner = ListofPoints->begin(); Runner != ListofPoints->end(); ++Runner)
    1130         DoeLog(1) && (eLog() << Verbose(1) << "  " << *(*Runner) << endl);
     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      }
    11311185    }
    11321186    delete (ListofPoints);
    11331187
    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     }
    11411188  }
    11421189  return flag;
    … …  
    32903337                        }
    32913338                      } else {
    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);
     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);
    32933340                      }
    32943341                    } else {
    … …  
    45904637
    45914638  DoLog(0) && (Log() << Verbose(0) << "FindAllDegeneratedTriangles() found " << DegeneratedTriangles->size() << " triangles:" << endl);
    4592   IndexToIndex::iterator it;
    4593   for (it = DegeneratedTriangles->begin(); it != DegeneratedTriangles->end(); it++)
     4639  for (IndexToIndex::iterator it = DegeneratedTriangles->begin(); it != DegeneratedTriangles->end(); it++)
    45944640    DoLog(0) && (Log() << Verbose(0) << (*it).first << " => " << (*it).second << endl);
    45954641
    … …  
    46094655  int count = 0;
    46104656
    4611   for (IndexToIndex::iterator TriangleKeyRunner = DegeneratedTriangles->begin(); TriangleKeyRunner != DegeneratedTriangles->end(); ++TriangleKeyRunner) {
     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
    46124665    finder = TrianglesOnBoundary.find(TriangleKeyRunner->first);
    46134666    if (finder != TrianglesOnBoundary.end())
    46144667      triangle = finder->second;
    46154668    else
    4616       break;
     4669      continue;
    46174670    finder = TrianglesOnBoundary.find(TriangleKeyRunner->second);
    46184671    if (finder != TrianglesOnBoundary.end())
    46194672      partnerTriangle = finder->second;
    46204673    else
    4621       break;
    4622 
     4674      continue;
     4675
     4676    // determine which lines are shared by the two triangles
    46234677    bool trianglesShareLine = false;
    46244678    for (int i = 0; i < 3; ++i)

  • src/tesselation.hpp

    rf0f1cc r51a5c8  
    138138    bool ContainsBoundaryPoint(const BoundaryPointSet * const point) const;
    139139    bool CheckConvexityCriterion() const;
     140    double CalculateConvexity() const;
    140141    class BoundaryPointSet *GetOtherEndpoint(const BoundaryPointSet * const point) const;
     142    class BoundaryTriangleSet *GetOtherTriangle(const BoundaryTriangleSet * const triangle) const;
    141143
    142144    class BoundaryPointSet *endpoints[2];
    … …  
    164166    bool ContainsBoundaryPoint(const TesselPoint * const point) const;
    165167    class BoundaryPointSet *GetThirdEndpoint(const BoundaryLineSet * const line) const;
     168    class BoundaryLineSet *GetThirdLine(const BoundaryPointSet * const point) const;
    166169    bool IsPresentTupel(const BoundaryPointSet * const Points[3]) const;
    167170    bool IsPresentTupel(const BoundaryTriangleSet * const T) const;

  • src/tesselationhelpers.cpp

    rf0f1cc r51a5c8  
    1212#include "info.hpp"
    1313#include "linkedcell.hpp"
     14#include "linearsystemofequations.hpp"
    1415#include "log.hpp"
    1516#include "tesselation.hpp"
    … …  
    185186  beta = M_PI - SideC.Angle(SideA);
    186187  gamma = M_PI - SideA.Angle(SideB);
    187   //Log() << Verbose(1) << "INFO: alpha = " << alpha/M_PI*180. << ", beta = " << beta/M_PI*180. << ", gamma = " << gamma/M_PI*180. << "." << endl;
     188  Log() << Verbose(1) << "INFO: alpha = " << alpha/M_PI*180. << ", beta = " << beta/M_PI*180. << ", gamma = " << gamma/M_PI*180. << "." << endl;
    188189  if (fabs(M_PI - alpha - beta - gamma) > HULLEPSILON) {
    189190    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);
    … …  
    198199  (*Center) += helper;
    199200  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;
    200238};
    201239
    … …  
    419457/** Calculates the volume of a general tetraeder.
    420458 * \param *a first vector
    421  * \param *a first vector
    422  * \param *a first vector
    423  * \param *a first vector
     459 * \param *b second vector
     460 * \param *c third vector
     461 * \param *d fourth vector
    424462 * \return \f$ \frac{1}{6} \cdot ((a-d) \times (a-c) \cdot  (a-b)) \f$
    425463 */
    … …  
    439477  volume = 1./6. * fabs(Point.ScalarProduct(TetraederVector[2]));
    440478  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 */
     488double 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;
    441499};
    442500
    … …  
    882940  class BoundaryPointSet *point = NULL;
    883941  class BoundaryLineSet *line = NULL;
    884 
    885   // calculate remaining concavity
     942  class BoundaryTriangleSet *triangle = NULL;
     943  double ConcavityPerLine = 0.;
     944  double ConcavityPerTriangle = 0.;
     945  double area = 0.;
     946  double totalarea = 0.;
     947
    886948  for (PointMap::const_iterator PointRunner = TesselStruct->PointsOnBoundary.begin(); PointRunner != TesselStruct->PointsOnBoundary.end(); PointRunner++) {
    887949    point = PointRunner->second;
    888950    DoLog(1) && (Log() << Verbose(1) << "INFO: Current point is " << *point << "." << endl);
    889     point->value = 0;
     951
     952    // calculate mean concavity over all connected line
     953    ConcavityPerLine = 0.;
    890954    for (LineMap::iterator LineRunner = point->lines.begin(); LineRunner != point->lines.end(); LineRunner++) {
    891955      line = LineRunner->second;
    892956      //Log() << Verbose(1) << "INFO: Current line of point " << *point << " is " << *line << "." << endl;
    893       if (!line->CheckConvexityCriterion())
    894         point->value += 1;
    895     }
    896   }
    897 };
    898 
     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 */
     998void 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};
    8991016
    9001017/** Checks whether each BoundaryLineSet in the Tesselation has two triangles.

  • src/tesselationhelpers.hpp

    rf0f1cc r51a5c8  
    4343/********************************************** definitions *********************************/
    4444
    45 #define HULLEPSILON 1e-10
     45#define HULLEPSILON 1e-9 //!< TODO: Get rid of HULLEPSILON, points to numerical instabilities
    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);
     57double CalculateAreaofGeneralTriangle(const Vector &A, const Vector &B, const Vector &C);
    5758double GetAngle(const Vector &point, const Vector &reference, const Vector &OrthogonalVector);
    5859
    … …  
    6869void WriteVrmlFile(ofstream * const vrmlfile, const Tesselation * const Tess, const PointCloud * const cloud);
    6970void CalculateConcavityPerBoundaryPoint(const Tesselation * const TesselStruct);
     71void CalculateConstrictionPerBoundaryPoint(const Tesselation * const TesselStruct, const Tesselation * const Convex);
    7072double DistanceToTrianglePlane(const Vector *x, const BoundaryTriangleSet * const triangle);
    7173

  • src/unittests/CountBondsUnitTest.cpp

    rf0f1cc r51a5c8  
    154154  Translator  = Vector(3,0,0);
    155155  TestMolecule2->Translate(&Translator);
    156   CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL) );
    157   CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, oxygen) );
     156  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
     157  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, oxygen, NULL) );
    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) );
     165  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, 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) );
     174  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, 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) );
     183  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, 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) );
     191  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, 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) );
     200  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, 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) );
     210  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, 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) );
     221  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
    222222  Translator = Vector(0,-3,0);
    223223  TestMolecule2->Translate(&Translator);

  • src/unittests/TestRunnerMain.cpp

    rf0f1cc r51a5c8  
    1717#include "../../../TestRunnerClient.h"
    1818#include "../../../TestRunnerClient.cpp"
     19
    1920#else
    20 #include "UnitTestMain.cpp"
    21 #endif
    2221
     22#include "unittests/UnitTestMain.cpp"
     23
     24#endif /* HAVE_ECUT */

  • src/unittests/UnitTestMain.cpp

    rf0f1cc r51a5c8  
    66 */
    77
    8 #include <cppunit/CompilerOutputter.h>
    9 #include <cppunit/extensions/TestFactoryRegistry.h>
    10 #include <cppunit/ui/text/TestRunner.h>
    11 
    128// include config.h
    139#ifdef HAVE_CONFIG_H
    1410#include <config.h>
    1511#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

    rf0f1cc r51a5c8  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=23, E=64, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    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
    8 1.2492 0.921941 -0.849545 3
    9 1.2492 0.921941 0.930455 3
    10 -2.4985 -1.22006 -0.849545 4
    11 -2.4985 -1.22006 0.930455 4
    12 2.4985 -1.22006 0.930455 4
    13 2.4985 -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
    17 4.6377 -0.336759 0.0404545 4
    18 3.7477 0.921941 -0.849545 4
    19 3.7477 0.921941 0.930455 4
    20 -7.27e-07 -0.590759 0.0404545 6
    21 -1.2492 0.292641 0.0404545 6
    22 1.2492 0.292641 0.0404545 6
    23 -2.4985 -0.590759 0.0404545 6
    24 2.4985 -0.590759 0.0404545 6
    25 -3.7477 0.292641 0.0404545 12
    26 3.7477 0.292641 0.0404545 12
     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
     81.2492 0.921941 -0.849545 18.7222
     91.2492 0.921941 0.930455 27.0641
     10-2.4985 -1.22006 -0.849545 19.9769
     11-2.4985 -1.22006 0.930455 27.4727
     122.4985 -1.22006 0.930455 19.9769
     132.4985 -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
     174.6377 -0.336759 0.0404545 10.6618
     183.7477 0.921941 -0.849545 18.5406
     193.7477 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
     221.2492 0.292641 0.0404545 20.1632
     23-2.4985 -0.590759 0.0404545 18.9798
     242.4985 -0.590759 0.0404545 18.9798
     25-3.7477 0.292641 0.0404545 39.5267
     263.7477 0.292641 0.0404545 23.2512
    2727
    282814 15 23
    … …  
    38385 18 19
    39394 5 18
     406 18 19
     413 6 18
    40423 4 18
    41433 4 18
    42 3 18 19
    43 3 6 19
    44444 18 22
    45454 13 22
    … …  
    484812 13 22
    494912 13 22
    50 16 19 23
    51 6 16 19
    52 14 16 23
    53 14 16 23
    54 9 14 23
    55 9 16 23
     506 19 23
     516 16 23
    565211 13 22
    575311 13 22
    … …  
    62588 11 22
    63598 12 22
     6014 16 23
     6114 16 23
     629 14 23
     639 16 23
     643 8 12
     651 3 8
     661 3 6
     671 6 9
     686 9 16
    64694 7 13
    65702 4 7
    … …  
    67722 5 10
    68735 10 15
    69 3 8 12
    70 1 3 8
    71 1 3 6
    72 1 6 9
    73 6 9 16
    747410 14 21
    75759 10 21
    … …  
    84842 17 20
    85852 7 20
    86 1 17 20
    87 1 8 20
    88867 8 20
    89877 8 20
    90887 11 20
    91898 11 20
     908 17 20
     911 8 17

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

    rf0f1cc r51a5c8  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    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
    8 1.2492 0.921941 -0.849545 0
    9 1.2492 0.921941 0.930455 0
    10 -2.4985 -1.22006 -0.849545 0
    11 -2.4985 -1.22006 0.930455 0
    12 2.4985 -1.22006 0.930455 0
    13 2.4985 -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
    17 4.6377 -0.336759 0.0404545 0
    18 3.7477 0.921941 -0.849545 0
    19 3.7477 0.921941 0.930455 0
     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
     81.2492 0.921941 -0.849545 -17.495
     91.2492 0.921941 0.930455 -17.4951
     10-2.4985 -1.22006 -0.849545 -13.1263
     11-2.4985 -1.22006 0.930455 -10.8961
     122.4985 -1.22006 0.930455 -13.1263
     132.4985 -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
     174.6377 -0.336759 0.0404545 -9.35473
     183.7477 0.921941 -0.849545 -11.4805
     193.7477 0.921941 0.930455 -9.24445
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 8 11 12
    30 3 8 12
    31 1 3 8
    32 1 3 6
    33 1 6 9
    34 6 9 16
    35 9 14 16
     297 11 13
     304 7 13
     312 4 7
     322 4 5
     332 5 10
     345 10 15
     3510 14 15
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 10 14 15
    43 5 10 15
    44 2 5 10
    45 2 4 5
    46 2 4 7
    47 4 7 13
    48 7 11 13
     429 14 16
     436 9 16
     441 6 9
     451 3 6
     461 3 8
     473 8 12
     488 11 12

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

    rf0f1cc r51a5c8  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    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
    8 1.2492 0.921941 -0.849545 0
    9 1.2492 0.921941 0.930455 0
    10 -2.4985 -1.22006 -0.849545 0
    11 -2.4985 -1.22006 0.930455 0
    12 2.4985 -1.22006 0.930455 0
    13 2.4985 -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
    17 4.6377 -0.336759 0.0404545 0
    18 3.7477 0.921941 -0.849545 0
    19 3.7477 0.921941 0.930455 0
     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
     81.2492 0.921941 -0.849545 -17.495
     91.2492 0.921941 0.930455 -17.4951
     10-2.4985 -1.22006 -0.849545 -13.1263
     11-2.4985 -1.22006 0.930455 -10.8961
     122.4985 -1.22006 0.930455 -13.1263
     132.4985 -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
     174.6377 -0.336759 0.0404545 -9.35473
     183.7477 0.921941 -0.849545 -11.4805
     193.7477 0.921941 0.930455 -9.24445
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 8 11 12
    30 3 8 12
    31 1 3 8
    32 1 3 6
    33 1 6 9
    34 6 9 16
    35 9 14 16
     297 11 13
     304 7 13
     312 4 7
     322 4 5
     332 5 10
     345 10 15
     3510 14 15
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 10 14 15
    43 5 10 15
    44 2 5 10
    45 2 4 5
    46 2 4 7
    47 4 7 13
    48 7 11 13
     429 14 16
     436 9 16
     441 6 9
     451 3 6
     461 3 8
     473 8 12
     488 11 12

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

    rf0f1cc r51a5c8  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    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
    8 1.2492 0.921941 -0.849545 0
    9 1.2492 0.921941 0.930455 0
    10 -2.4985 -1.22006 -0.849545 0
    11 -2.4985 -1.22006 0.930455 0
    12 2.4985 -1.22006 0.930455 0
    13 2.4985 -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
    17 4.6377 -0.336759 0.0404545 0
    18 3.7477 0.921941 -0.849545 0
    19 3.7477 0.921941 0.930455 0
     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
     81.2492 0.921941 -0.849545 -17.495
     91.2492 0.921941 0.930455 -17.4951
     10-2.4985 -1.22006 -0.849545 -13.1263
     11-2.4985 -1.22006 0.930455 -10.8961
     122.4985 -1.22006 0.930455 -13.1263
     132.4985 -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
     174.6377 -0.336759 0.0404545 -9.35473
     183.7477 0.921941 -0.849545 -11.4805
     193.7477 0.921941 0.930455 -9.24445
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 8 11 12
    30 3 8 12
    31 1 3 8
    32 1 3 6
    33 1 6 9
    34 6 9 16
    35 9 14 16
     297 11 13
     304 7 13
     312 4 7
     322 4 5
     332 5 10
     345 10 15
     3510 14 15
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 10 14 15
    43 5 10 15
    44 2 5 10
    45 2 4 5
    46 2 4 7
    47 4 7 13
    48 7 11 13
     429 14 16
     436 9 16
     441 6 9
     451 3 6
     461 3 8
     473 8 12
     488 11 12

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

    rf0f1cc r51a5c8  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    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
    8 1.2492 0.921941 -0.849545 0
    9 1.2492 0.921941 0.930455 0
    10 -2.4985 -1.22006 -0.849545 0
    11 -2.4985 -1.22006 0.930455 0
    12 2.4985 -1.22006 0.930455 0
    13 2.4985 -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
    17 4.6377 -0.336759 0.0404545 0
    18 3.7477 0.921941 -0.849545 0
    19 3.7477 0.921941 0.930455 0
     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
     81.2492 0.921941 -0.849545 -17.495
     91.2492 0.921941 0.930455 -17.4951
     10-2.4985 -1.22006 -0.849545 -13.1263
     11-2.4985 -1.22006 0.930455 -10.8961
     122.4985 -1.22006 0.930455 -13.1263
     132.4985 -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
     174.6377 -0.336759 0.0404545 -9.35473
     183.7477 0.921941 -0.849545 -11.4805
     193.7477 0.921941 0.930455 -9.24445
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 8 11 12
    30 3 8 12
    31 1 3 8
    32 1 3 6
    33 1 6 9
    34 6 9 16
    35 9 14 16
     297 11 13
     304 7 13
     312 4 7
     322 4 5
     332 5 10
     345 10 15
     3510 14 15
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 10 14 15
    43 5 10 15
    44 2 5 10
    45 2 4 5
    46 2 4 7
    47 4 7 13
    48 7 11 13
     429 14 16
     436 9 16
     441 6 9
     451 3 6
     461 3 8
     473 8 12
     488 11 12

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

    rf0f1cc r51a5c8  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    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
    8 1.2492 0.921941 -0.849545 0
    9 1.2492 0.921941 0.930455 0
    10 -2.4985 -1.22006 -0.849545 0
    11 -2.4985 -1.22006 0.930455 0
    12 2.4985 -1.22006 0.930455 0
    13 2.4985 -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
    17 4.6377 -0.336759 0.0404545 0
    18 3.7477 0.921941 -0.849545 0
    19 3.7477 0.921941 0.930455 0
     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
     81.2492 0.921941 -0.849545 -17.495
     91.2492 0.921941 0.930455 -17.4951
     10-2.4985 -1.22006 -0.849545 -13.1263
     11-2.4985 -1.22006 0.930455 -10.8961
     122.4985 -1.22006 0.930455 -13.1263
     132.4985 -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
     174.6377 -0.336759 0.0404545 -9.35473
     183.7477 0.921941 -0.849545 -11.4805
     193.7477 0.921941 0.930455 -9.24445
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 8 11 12
    30 3 8 12
    31 1 3 8
    32 1 3 6
    33 1 6 9
    34 6 9 16
    35 9 14 16
     297 11 13
     304 7 13
     312 4 7
     322 4 5
     332 5 10
     345 10 15
     3510 14 15
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 10 14 15
    43 5 10 15
    44 2 5 10
    45 2 4 5
    46 2 4 7
    47 4 7 13
    48 7 11 13
     429 14 16
     436 9 16
     441 6 9
     451 3 6
     461 3 8
     473 8 12
     488 11 12

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

    rf0f1cc r51a5c8  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="heptan", N=16, E=28, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    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
    8 1.2492 0.921941 -0.849545 0
    9 1.2492 0.921941 0.930455 0
    10 -2.4985 -1.22006 -0.849545 0
    11 -2.4985 -1.22006 0.930455 0
    12 2.4985 -1.22006 0.930455 0
    13 2.4985 -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
    17 4.6377 -0.336759 0.0404545 0
    18 3.7477 0.921941 -0.849545 0
    19 3.7477 0.921941 0.930455 0
     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
     81.2492 0.921941 -0.849545 -17.495
     91.2492 0.921941 0.930455 -17.4951
     10-2.4985 -1.22006 -0.849545 -13.1263
     11-2.4985 -1.22006 0.930455 -10.8961
     122.4985 -1.22006 0.930455 -13.1263
     132.4985 -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
     174.6377 -0.336759 0.0404545 -9.35473
     183.7477 0.921941 -0.849545 -11.4805
     193.7477 0.921941 0.930455 -9.24445
    2020
    212114 15 16
    … …  
    27273 12 13
    282811 12 13
    29 8 11 12
    30 3 8 12
    31 1 3 8
    32 1 3 6
    33 1 6 9
    34 6 9 16
    35 9 14 16
     297 11 13
     304 7 13
     312 4 7
     322 4 5
     332 5 10
     345 10 15
     3510 14 15
    36369 10 14
    37372 9 10
    … …  
    40401 7 8
    41417 8 11
    42 10 14 15
    43 5 10 15
    44 2 5 10
    45 2 4 5
    46 2 4 7
    47 4 7 13
    48 7 11 13
     429 14 16
     436 9 16
     441 6 9
     451 3 6
     461 3 8
     473 8 12
     488 11 12

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

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

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

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

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

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

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

    rf0f1cc r51a5c8  
    22VARIABLES = "X" "Y" "Z" "U"
    33ZONE T="test", N=44, E=86, DATAPACKING=POINT, ZONETYPE=FETRIANGLE
    4 6.9077 1.1106 0.1214 1
    5 0.3612 -3.628 1.323 1
    6 0.4884 -3.5983 -0.4521 3
    7 1.4985 -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
    11 1.7627 -1.4479 -0.8349 4
    12 -1.003 -1.3584 -2.8848 2
    13 0.0217 -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
    17 1.0353 0.1785 2.542 3
    18 1.6325 -1.3323 1.8306 2
    19 0.7271 1.177 0.3594 3
    20 1.3374 -0.2942 -2.961 2
    21 0.6036 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
    26 3.191 1.3217 -2.8354 1
    27 -4.0905 0.6312 1.6028 3
    28 2.8131 1.4776 2.5103 0
    29 3.9137 2.2936 1.3739 0
    30 2.159 2.5738 1.2698 5
    31 3.6606 -0.4593 2.1396 2
    32 3.2007 -1.4419 0.7311 4
    33 -3.3002 2.3589 0.0094 8
    34 -4.377 1.6962 -1.2433 3
    35 5.2593 1.4547 -1.7445 0
    36 4.6863 2.7674 -0.6775 0
    37 5.746 -0.9031 1.204 0
    38 5.1212 -0.8867 -0.4582 4
    39 -5.2641 2.8314 1.4476 0
    40 5.2727 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
    47 7.1391 2.0447 0.0264 0
     46.9077 1.1106 0.1214 -6.99715
     50.3612 -3.628 1.323 6.00416
     60.4884 -3.5983 -0.4521 11.8428
     71.4985 -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
     111.7627 -1.4479 -0.8349 7.15053
     12-1.003 -1.3584 -2.8848 32.043
     130.0217 -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
     171.0353 0.1785 2.542 48.8869
     181.6325 -1.3323 1.8306 1.44108
     190.7271 1.177 0.3594 27.9872
     201.3374 -0.2942 -2.961 13.6459
     210.6036 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
     263.191 1.3217 -2.8354 -10.5968
     27-4.0905 0.6312 1.6028 21.8745
     282.8131 1.4776 2.5103 -0.774194
     293.9137 2.2936 1.3739 -2.51806
     302.159 2.5738 1.2698 151.494
     313.6606 -0.4593 2.1396 2.60004
     323.2007 -1.4419 0.7311 2.29272
     33-3.3002 2.3589 0.0094 461.065
     34-4.377 1.6962 -1.2433 43.4649
     355.2593 1.4547 -1.7445 -6.26082
     364.6863 2.7674 -0.6775 -8.55931
     375.746 -0.9031 1.204 -1.29544
     385.1212 -0.8867 -0.4582 31.5177
     39-5.2641 2.8314 1.4476 21.5516
     405.2727 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
     477.1391 2.0447 0.0264 -7.88713
    4848
    49491 32 44

  • tests/regression/testsuite-filling.at

    rf0f1cc r51a5c8  
    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], 0, [stdout], [stderr])
     20AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -u 1.3 --molecule-by-id 0], 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

    rf0f1cc r51a5c8  
    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 1], 0, [stdout], [stderr])
     63AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -m 0], 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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