Changes in / [ed58ad:cd032d]


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Files:
20 added
18 edited

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  • configure.ac

    red58ad rcd032d  
    3434#AX_BOOST_PROGRAM_OPTIONS
    3535#AX_BOOST_SERIALIZATION
     36
     37#QT4 libraries
     38gw_CHECK_QT4
     39AX_CHECK_GLU
     40AC_MSG_NOTICE(["GLU_CFLAGS: $GLU_CFLAGS, GLU_CXXFLAGS: $GLU_CXXFLAGS, GLU_LDFLAGS: $GLU_LDFLAGS, GLU_LIBS: $GLU_LIBS"])
     41
    3642
    3743# Checks for header files.

  • doc/Doxyfile

    red58ad rcd032d  
    127127#---------------------------------------------------------------------------
    128128SOURCE_BROWSER         = YES
    129 INLINE_SOURCES         = NO
    130 STRIP_CODE_COMMENTS    = YES
     129INLINE_SOURCES         = YES
     130STRIP_CODE_COMMENTS    = NO
    131131REFERENCED_BY_RELATION = NO
    132132REFERENCES_RELATION    = NO

  • doc/class structure.uxf

    red58ad rcd032d  
    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/Process.cpp

    red58ad rcd032d  
    3838
    3939int Process::getCurrStep(){
    40   OBSERVE;
    4140  return currStep;
    4241}
    4342
    4443void Process::setCurrStep(int _currStep){
     44  OBSERVE;
    4545  currStep = _currStep;
    4646}
    … …  
    5252    return 0;
    5353}
    54 
    5554int Process::getMaxSteps(){
    5655  return maxSteps;

  • src/Actions/small_actions.hpp

    red58ad rcd032d  
    2525};
    2626
    27 
    2827#endif // _SMALL_ACTIONS_HPP

  • src/Makefile.am

    red58ad rcd032d  
    88ANALYSISHEADER = analysis_bonds.hpp analysis_correlation.hpp
    99
    10 ACTIONSSOURCE = Actions/Action.cpp Actions/Process.cpp Actions/MethodAction.cpp Actions/ActionSequence.cpp Actions/MakroAction.cpp Actions/ErrorAction.cpp Actions/small_actions.cpp Actions/ManipulateAtomsProcess.cpp Actions/ActionRegistry.cpp
    11 ACTIONSHEADER = Actions/Action.hpp Actions/Process.hpp Actions/Calculation.hpp Actions/Calculation_impl.hpp Actions/MethodAction.hpp Actions/ActionSequence.hpp Actions/MakroAction.hpp Actions/ErrorAction.hpp Actions/small_actions.hpp Actions/ManipulateAtomsProcess.hpp Actions/ActionRegistry.hpp
     10# only include Actions that are free of user interaction at this point
     11# the UIFactory et. al. wont be known for the libmolecuilder, so the user interaction cannot be done.
     12ACTIONSSOURCE = Actions/Action.cpp Actions/Process.cpp Actions/MethodAction.cpp Actions/ActionSequence.cpp Actions/MakroAction.cpp Actions/ManipulateAtomsProcess.cpp Actions/ActionRegistry.cpp
     13ACTIONSHEADER = Actions/Action.hpp Actions/Process.hpp Actions/Calculation.hpp Actions/Calculation_impl.hpp Actions/MethodAction.hpp Actions/ActionSequence.hpp Actions/MakroAction.hpp Actions/ManipulateAtomsProcess.hpp Actions/ActionRegistry.hpp
     14
     15# All actions that need user interaction go here
     16MENUACTIONSSOURCE = Actions/ErrorAction.cpp Actions/small_actions.cpp
     17MENUACTIONSHEADER = Actions/ErrorAction.hpp Actions/small_actions.hpp
    1218
    1319PATTERNSOURCE = Patterns/Observer.cpp
    … …  
    2228MENUHEADER = Menu/Menu.hpp Menu/TextMenu.hpp Menu/MenuItem.hpp Menu/SubMenuItem.hpp Menu/ActionMenuItem.hpp Menu/SeperatorItem.hpp Menu/DisplayMenuItem.hpp
    2329
    24 UISOURCE = ${ACTIONSSOURCE} ${VIEWSOURCE} ${MENUSOURCE} UIElements/UIFactory.cpp UIElements/TextUIFactory.cpp UIElements/MainWindow.cpp UIElements/TextWindow.cpp UIElements/TextStatusIndicator.cpp UIElements/Dialog.cpp UIElements/TextDialog.cpp
    25 UIHEADER = ${ACTIONSHEADER} ${VIEWHEADER} ${MENUHEADER} UIElements/UIFactory.hpp UIElements/TextUIFactory.hpp UIElements/MainWindow.hpp UIElements/TextWindow.hpp UIElements/TextStatusIndicator.hpp UIElements/Dialog.hpp UIElements/TextDialog.hpp
     30UISOURCE = ${MENUACTIONSSOURCE} ${VIEWSOURCE} ${MENUSOURCE} UIElements/TextUIFactory.cpp UIElements/MainWindow.cpp UIElements/TextWindow.cpp UIElements/Dialog.cpp UIElements/TextDialog.cpp UIElements/TextStatusIndicator.cpp
     31UIHEADER = ${MENUACTIONSHEADER} ${VIEWHEADER} ${MENUHEADER} UIElements/TextUIFactory.hpp UIElements/MainWindow.hpp UIElements/TextWindow.hpp UIElements/Dialog.hpp UIElements/TextDialog.hpp UIElements/TextStatusIndicator.hpp
     32
     33FACTORYSOURCE = UIElements/UIFactory.cpp
     34FACTORYHEADER = UIElements/UIFactory.hpp
    2635
    2736# all these files are only used for legacy reasons while the transition is in progress
    … …  
    3039LEGACYSOURCE = Legacy/oldmenu.cpp
    3140LEGACYHEADER = Legacy/oldmenu.hpp
     41
     42QTUIMOC_HEADER = UIElements/QT4/QTDialog.hpp \
     43                                 UIElements/QT4/QTMainWindow.hpp \
     44                                 Menu/QT4/QTMenu.hpp \
     45                                 Views/QT4/QTWorldView.hpp \
     46                                 Views/QT4/GLMoleculeView.hpp \
     47                                 Views/QT4/QTMoleculeView.hpp \
     48                                 Views/QT4/QTStatusBar.hpp
     49 
     50QTUIMOC_TARGETS = QTMainWindow.moc.cpp \
     51                      QTMenu.moc.cpp\
     52                      QTDialog.moc.cpp \
     53                      QTWorldView.moc.cpp \
     54                      GLMoleculeView.moc.cpp \
     55                      QTMoleculeView.moc.cpp \
     56                      QTStatusBar.moc.cpp
    3257
    3358DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
    … …  
    4368                                   Descriptors/MoleculeIdDescriptor.hpp
    4469
    45 SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} ${PATTERNSOURCE} ${UISOURCE} ${DESCRIPTORSOURCE} ${LEGACYSOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp info.cpp leastsquaremin.cpp linkedcell.cpp lists.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp World.cpp WorldIterators.cpp
    46 HEADER = ${ANALYSISHEADER} ${ATOMHEADER} ${PATTERNHEADER} ${UIHEADER} ${DESCRIPTORHEADER} ${LEGACYHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp graph.hpp helpers.hpp info.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp World.hpp
     70QTUISOURCE = ${QTUIMOC_TARGETS} \
     71             UIElements/QT4/QTMainWindow.cpp \
     72             UIElements/QT4/QTDialog.cpp \
     73             UIElements/QT4/QTUIFactory.cpp \
     74             Menu/QT4/QTMenu.cpp \
     75             Views/QT4/QTWorldView.cpp \
     76             Views/QT4/GLMoleculeView.cpp \
     77             Views/QT4/QTMoleculeView.cpp \
     78             Views/QT4/QTStatusBar.cpp
     79             
     80QTUIHEADER = ${QTUIMOC_HEADER} UIElements/QT4/QTUIFactory.hpp
     81
     82QTUI_DEFS =
     83
     84SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} ${PATTERNSOURCE} ${ACTIONSSOURCE} ${DESCRIPTORSOURCE}  bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp info.cpp leastsquaremin.cpp linkedcell.cpp lists.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp World.cpp WorldIterators.cpp
     85HEADER = ${ANALYSISHEADER} ${ATOMHEADER} ${PATTERNHEADER} ${ACTIONSHEADER} ${DESCRIPTORHEADER} ${LEGACYHEADER} bond.hpp bondgraph.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp errorlogger.hpp graph.hpp helpers.hpp info.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp log.hpp logger.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp World.hpp
    4786
    4887BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
     88GUI_LIBS = ${QT_LDADD} ${QT_LIB_GUI} -lQtOpenGL ${GLU_LIBS}
    4989INCLUDES = -I$(top_srcdir)/src/unittests
    5090
    51 noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a
    52 bin_PROGRAMS = molecuilder joiner analyzer
     91noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a libmenu.a
     92bin_PROGRAMS = molecuilder molecuildergui joiner analyzer
    5393molecuilderdir = ${bindir}
     94
    5495libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
     96
     97libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER}
     98
    5599libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
     100
    56101molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
    57 molecuilder_LDFLAGS = $(BOOST_LDFLAGS)
    58 molecuilder_SOURCES = builder.cpp
    59 molecuilder_LDADD = libmolecuilder.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
     102
     103molecuilder_CXXFLAGS = $(BOOST_CPPFLAGS)
     104#molecuilder_CXXFLAGS += -DNO_CACHING
     105molecuilder_LDFLAGS = $(BOOST_LIB)
     106molecuilder_SOURCES = ${FACTORYSOURCE} ${LEGACYSOURCE} builder.cpp
     107molecuilder_SOURCES += $(srcdir)/version.c
     108molecuilder_LDADD = libmolecuilder.a libgslwrapper.a libmenu.a ${BOOST_THREAD_LIB}
     109
     110#Stuff for building the GUI using QT
     111molecuildergui_SOURCES = ${QTUISOURCE} ${FACTORYSOURCE} ${LEGACYSOURCE} builder.cpp
     112molecuildergui_SOURCES += $(srcdir)/version.c
     113molecuildergui_CXXFLAGS = ${QT_CXXFLAGS} ${GLU_CXXFLAGS} -DUSE_GUI_QT
     114molecuildergui_LDFLAGS = $(BOOST_LIB) ${QT_LDFLAGS} ${GLU_LDFLAGS}
     115molecuildergui_LDADD = libmolecuilder.a libgslwrapper.a libmenu.a ${BOOST_THREAD_LIB} ${GUI_LIBS}
     116
    60117joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
    61118joiner_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
     119
    62120analyzer_SOURCES = analyzer.cpp datacreator.cpp parser.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp
    63121analyzer_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    64122
     123#Rules needed for QT4
     124# UI-Files are scattered throughout several subdirectories
     125# Therfore `%'-rules do not seem to work
     126#Quick fix to get it done otherwise
     127${QTUIMOC_TARGETS}: ${QTUIMOC_HEADER}
     128        list='$(QTUIMOC_HEADER)'; for header in $$list; do \
     129        echo "Making mocfile for $$header"; \
     130        target=`basename $$header | sed "s/\(.*\)\..*/\1.moc.cpp/"`;\
     131        $(MOC) $(srcdir)/$$header -o $$target \
     132        || eval $$failcom; \
     133        done;
     134
     135MOSTLYCLEANFILES = ${QTUIMOC_TARGETS}
     136       
    65137#EXTRA_DIST = ${molecuilder_DATA}
    66138
    … …  
    79151        echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
    80152
    81 molecuilder_SOURCES += $(srcdir)/version.c
     153

  • src/UIElements/Dialog.cpp

    red58ad rcd032d  
    3131
    3232bool Dialog::display(){
     33  if(checkAll()){
     34    setAll();
     35    return true;
     36  }
     37  else{
     38    return false;
     39  }
     40}
     41
     42bool Dialog::checkAll(){
    3343  list<Query*>::iterator iter;
    3444  bool retval = true;
    … …  
    3949      break;
    4050  }
    41   if (retval){
    42     // if all queries succeeded we can set the targets to appropriate values
    43     for(iter=queries.begin(); iter!=queries.end(); iter++) {
    44       (*iter)->setResult();
    45     }
     51  return retval;
     52}
     53
     54void Dialog::setAll(){
     55  list<Query*>::iterator iter;
     56  for(iter=queries.begin(); iter!=queries.end(); iter++) {
     57    (*iter)->setResult();
    4658  }
    47   return retval;
    4859}
    4960
    … …  
    7687
    7788Dialog::StringQuery::StringQuery(string title,string *_target) :
    78     Query(title), target(_target)
     89    Query(title),
     90    target(_target),
     91    tmp("")
    7992{}
    8093
    … …  
    133146  *target = *tmp;
    134147}
     148
     149// Element Queries
     150Dialog::ElementQuery::ElementQuery(std::string title, element **_target) :
     151  Query(title),
     152  target(_target),
     153  tmp(0)
     154  {}
     155
     156Dialog::ElementQuery::~ElementQuery(){}
     157
     158void Dialog::ElementQuery::setResult(){
     159  *target=tmp;
     160}

  • src/UIElements/Dialog.hpp

    red58ad rcd032d  
    1515class molecule;
    1616class Vector;
     17class element;
    1718
    1819class Dialog
    … …  
    2728  virtual void queryMolecule(const char*,molecule**,MoleculeListClass*)=0;
    2829  virtual void queryVector(const char*,Vector *,const double *const,bool)=0;
     30  virtual void queryElement(const char*,element **)=0;
    2931
    3032  virtual bool display();
     33
     34  virtual bool checkAll();
     35  virtual void setAll();
    3136
    3237protected:
    … …  
    4550  public:
    4651    Query(std::string _title);
    47     ~Query();
     52    virtual ~Query();
    4853    virtual bool handle()=0;
    4954    virtual void setResult()=0;
    … …  
    5863  public:
    5964    IntQuery(std::string title,int *_target);
    60     ~IntQuery();
     65    virtual ~IntQuery();
    6166    virtual bool handle()=0;
    6267    virtual void setResult();
    … …  
    7075  public:
    7176    DoubleQuery(std::string title,double *_target);
    72     ~DoubleQuery();
     77    virtual ~DoubleQuery();
    7378    virtual bool handle()=0;
    7479    virtual void setResult();
    … …  
    8287  public:
    8388    StringQuery(std::string title,std::string *_target);
    84     ~StringQuery();
     89    virtual ~StringQuery();
    8590    virtual bool handle()=0;
    8691    virtual void setResult();
    … …  
    95100  public:
    96101    MoleculeQuery(std::string title, molecule **_target, MoleculeListClass *_molecules);
    97     ~MoleculeQuery();
     102    virtual ~MoleculeQuery();
    98103    virtual bool handle()=0;
    99104    virtual void setResult();
    … …  
    108113  public:
    109114      VectorQuery(std::string title,Vector *_target,const double *const _cellSize,bool _check);
    110       ~VectorQuery();
     115      virtual ~VectorQuery();
    111116      virtual bool handle()=0;
    112117      virtual void setResult();
    … …  
    119124  };
    120125
     126  class ElementQuery : public Query {
     127  public:
     128    ElementQuery(std::string title, element**_target);
     129    virtual ~ElementQuery();
     130    virtual bool handle()=0;
     131    virtual void setResult();
     132  protected:
     133    element *tmp;
     134  private:
     135    element **target;
     136  };
     137
    121138void registerQuery(Query* query);
    122139

  • src/UIElements/TextDialog.cpp

    red58ad rcd032d  
    1010#include "UIElements/TextDialog.hpp"
    1111
     12#include "World.hpp"
     13#include "periodentafel.hpp"
    1214#include "atom.hpp"
    1315#include "molecule.hpp"
    … …  
    4547void TextDialog::queryVector(const char* title, Vector *target,const double *const cellSize, bool check) {
    4648  registerQuery(new VectorTextQuery(title,target,cellSize,check));
     49}
     50
     51void TextDialog::queryElement(const char* title, element **target){
     52  registerQuery(new ElementTextQuery(title,target));
    4753}
    4854
    … …  
    113119
    114120bool TextDialog::VectorTextQuery::handle() {
     121 Log() << Verbose(0) << getTitle();
    115122 tmp->AskPosition(cellSize,check);
    116123 return true;
    117124}
     125
     126
     127TextDialog::ElementTextQuery::ElementTextQuery(std::string title, element **target) :
     128    Dialog::ElementQuery(title,target)
     129{}
     130
     131TextDialog::ElementTextQuery::~ElementTextQuery()
     132{}
     133
     134bool TextDialog::ElementTextQuery::handle() {
     135  int Z;
     136  Log() << Verbose(0) << getTitle();
     137  cin >> Z;
     138  tmp = World::getInstance().getPeriode()->FindElement(Z);
     139  return tmp;
     140}

  • src/UIElements/TextDialog.hpp

    red58ad rcd032d  
    2424  virtual void queryMolecule(const char*,molecule**,MoleculeListClass*);
    2525  virtual void queryVector(const char*,Vector *,const double * const,bool);
     26  virtual void queryElement(const char*,element **);
    2627
    2728protected:
    … …  
    3031  public:
    3132    IntTextQuery(std::string title, int *_target);
    32     ~IntTextQuery();
     33    virtual ~IntTextQuery();
    3334    virtual bool handle();
    3435  };
    … …  
    3738  public:
    3839    DoubleTextQuery(std::string title, double *_target);
    39     ~DoubleTextQuery();
     40    virtual ~DoubleTextQuery();
    4041    virtual bool handle();
    4142  };
    … …  
    4445  public:
    4546    StringTextQuery(std::string title, std::string *_target);
    46     ~StringTextQuery();
     47    virtual ~StringTextQuery();
    4748    virtual bool handle();
    4849  };
    … …  
    5152  public:
    5253    MoleculeTextQuery(std::string title, molecule **_target, MoleculeListClass *_molecules);
    53     ~MoleculeTextQuery();
     54    virtual ~MoleculeTextQuery();
    5455    virtual bool handle();
    5556  };
    … …  
    5859  public:
    5960    VectorTextQuery(std::string title,Vector *_target,const double *const _cellSize,bool _check);
    60     ~VectorTextQuery();
     61    virtual ~VectorTextQuery();
     62    virtual bool handle();
     63  };
     64
     65  class ElementTextQuery : public Dialog::ElementQuery {
     66  public:
     67    ElementTextQuery(std::string title, element **_target);
     68    virtual ~ElementTextQuery();
    6169    virtual bool handle();
    6270  };

  • src/UIElements/TextUIFactory.hpp

    red58ad rcd032d  
    1313class TextUIFactory : public UIFactory
    1414{
    15 friend class UIFactory;
     15  friend class UIFactory;
    1616
    1717public:

  • src/UIElements/UIFactory.cpp

    red58ad rcd032d  
    1313// all factories that can be used:
    1414#include "UIElements/TextUIFactory.hpp"
     15#ifdef USE_GUI_QT
     16#include "UIElements/QT4/QTUIFactory.hpp"
     17#endif
    1518
    1619UIFactory::UIFactory()
    … …  
    3033      setInstance(new TextUIFactory());
    3134      break;
    32 
     35#ifdef USE_GUI_QT
     36    case QT4 :
     37      setInstance(new QTUIFactory());
     38      break;
     39#endif
    3340    default:
    3441      assert(0 && "No such Factory in stock");

  • src/UIElements/UIFactory.hpp

    red58ad rcd032d  
    3131
    3232public:
    33   enum InterfaceTypes {Text};
     33  enum InterfaceTypes {
     34    Text,
     35#ifdef USE_GUI_QT
     36    QT4
     37#endif
     38};
    3439  virtual ~UIFactory();
    3540

  • src/builder.cpp

    red58ad rcd032d  
    451451  mol->Mirror((const Vector *)&n);
    452452};
     453>>>>>>> MenuRefactoring:molecuilder/src/builder.cpp
    453454
    454455/** Submenu for removing the atoms from the molecule.
    … …  
    22052206        mol = World::getInstance().createMolecule();
    22062207        World::getInstance().getMolecules()->insert(mol);
    2207         cout << "Molecule created" << endl;
    22082208        if(mol->cell_size[0] == 0.){
    22092209            Log() << Verbose(0) << "enter lower tridiagonal form of basis matrix" << endl << endl;
    … …  
    22172217
    22182218    {
    2219       cout << ESPACKVersion << endl;
    2220 
    22212219      setVerbosity(0);
    22222220
    … …  
    22242222      populaters.MakeEditMoleculesMenu = populateEditMoleculesMenu;
    22252223
     2224#ifdef USE_GUI_QT
     2225      UIFactory::makeUserInterface(UIFactory::QT4);
     2226#else
     2227      cout << ESPACKVersion << endl;
    22262228      UIFactory::makeUserInterface(UIFactory::Text);
     2229#endif
    22272230      MainWindow *mainWindow = UIFactory::getInstance().makeMainWindow(populaters,World::getInstance().getMolecules(), configuration, World::getInstance().getPeriode(), ConfigFileName);
    22282231      mainWindow->display();
     2232
    22292233      delete mainWindow;
    22302234    }

  • src/defs.hpp

    red58ad rcd032d  
    8585#define STD_SEPERATOR_SPACER '-'
    8686
    87 // some types used to set template parameters
    88 struct true_type{
    89   enum{value=1};
    90 };
    91 struct false_type{
    92   enum{value = 0};
    93 };
     87#define MOLECUILDER_NAME "Molecuilder"
    9488
    9589#endif /*DEFS_HPP_*/

  • src/unittests/Makefile.am

    red58ad rcd032d  
    44AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
    55
    6 MENUTESTS = ActionSequenceTest
     6MENUTESTS = ActionSequenceTest
     7
    78
    89TESTS = \
    … …  
    3637  ${MENUTESTS}
    3738 
    38 
    39      
    40  
     39 
    4140check_PROGRAMS = $(TESTS)
    4241noinst_PROGRAMS = $(TESTS) TestRunner

  • src/vector.cpp

    red58ad rcd032d  
    2020#include <gsl/gsl_permutation.h>
    2121#include <gsl/gsl_vector.h>
     22
     23#include <cassert>
    2224
    2325/************************************ Functions for class vector ************************************/
    … …  
    659661  return x;
    660662};
     663
     664Vector& Vector::operator=(const Vector& src) {
     665  CopyVector(src);
     666  return *this;
     667}
     668
     669double& Vector::operator[](int i){
     670  assert(i<NDIM && "Invalid Vector dimension requested");
     671  return x[i];
     672}
    661673
    662674/** Prints a 3dim vector.

  • src/vector.hpp

    red58ad rcd032d  
    8080  void WrapPeriodically(const double * const M, const double * const Minv);
    8181
     82  Vector& operator=(const Vector &src);
     83  double& operator[](int i);
     84
    8285};
    8386
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