Changes in / [cd032d:ed58ad]


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Files:
20 deleted
18 edited

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  • configure.ac

    rcd032d red58ad  
    3434#AX_BOOST_PROGRAM_OPTIONS
    3535#AX_BOOST_SERIALIZATION
    36 
    37 #QT4 libraries
    38 gw_CHECK_QT4
    39 AX_CHECK_GLU
    40 AC_MSG_NOTICE(["GLU_CFLAGS: $GLU_CFLAGS, GLU_CXXFLAGS: $GLU_CXXFLAGS, GLU_LDFLAGS: $GLU_LDFLAGS, GLU_LIBS: $GLU_LIBS"])
    41 
    4236
    4337# Checks for header files.

  • doc/Doxyfile

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

  • doc/class structure.uxf

    rcd032d red58ad  
    2121
    2222
    23 // This text will be stored with each diagram;  use it for notes.</help_text><zoom_level>7</zoom_level><element><type>com.umlet.element.base.Class</type><coordinates><x>1855</x><y>210</y><w>147</w><h>70</h></coordinates><panel_attributes>AtomInfo
     23// This text will be stored with each diagram;  use it for notes.</help_text><zoom_level>7</zoom_level><element><type>com.umlet.element.base.Class</type><coordinates><x>1855</x><y>294</y><w>147</w><h>70</h></coordinates><panel_attributes>AtomInfo
    2424--
    2525-x,v,F: Vector
    … …  
    2828#AtomInfo();
    2929#~AtomInfo();
    30 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1645</x><y>231</y><w>223</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>210;21;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1274</x><y>63</y><w>392</w><h>259</h></coordinates><panel_attributes>Element
     30</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1645</x><y>315</y><w>223</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>210;21;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1274</x><y>147</y><w>392</w><h>259</h></coordinates><panel_attributes>Element
    3131--
    3232mass: double
    … …  
    4949#~element();
    5050#Output(ofstream * const out) const: bool
    51 #Checkout(ofstream * const out, const int No, const int NoOfAtoms) const: bool</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1960</x><y>448</y><w>280</w><h>161</h></coordinates><panel_attributes>BondedParticle
     51#Checkout(ofstream * const out, const int No, const int NoOfAtoms) const: bool</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1960</x><y>532</y><w>280</w><h>161</h></coordinates><panel_attributes>BondedParticle
    5252--
    5353--
    … …  
    6363#OutputBondOfAtom() const
    6464#OutputAdjacency(ofstream *AdjacencyFile) const
    65 #OutputOrder(ofstream *file) const</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2184</x><y>259</y><w>258</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>245;21;245;154;21;154;21;189</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1925</x><y>259</y><w>293</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-
    66 </panel_attributes><additional_attributes>21;21;21;154;280;154;280;189</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2184</x><y>259</y><w>34</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;189</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2359</x><y>210</y><w>147</w><h>70</h></coordinates><panel_attributes>BondedParticleInfo
     65#OutputOrder(ofstream *file) const</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2184</x><y>343</y><w>258</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>245;21;245;154;21;154;21;189</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1925</x><y>343</y><w>293</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-
     66</panel_attributes><additional_attributes>21;21;21;154;280;154;280;189</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2184</x><y>343</y><w>34</w><h>202</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;189</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2359</x><y>294</y><w>147</w><h>70</h></coordinates><panel_attributes>BondedParticleInfo
    6767--
    6868AdaptiveOrder: unsigned char
    … …  
    7171#BondedParticleInfo()
    7272#~BondedParticleInfo()
    73 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2079</x><y>196</y><w>217</w><h>84</h></coordinates><panel_attributes>ParticleInfo
     73</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2079</x><y>280</y><w>217</w><h>84</h></coordinates><panel_attributes>ParticleInfo
    7474--
    7575nr: int
    … …  
    7979#~ParticleInfo()
    8080#ostream &amp; operator &lt;&lt; (ostream &amp;ost) const
    81 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2485</x><y>231</y><w>174</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;161;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2646</x><y>161</y><w>147</w><h>133</h></coordinates><panel_attributes>BondList
     81</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2485</x><y>315</y><w>174</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;161;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2646</x><y>245</y><w>147</w><h>133</h></coordinates><panel_attributes>BondList
    8282{Some Properties}
    8383--
    … …  
    9090Responsibilities
    9191-- Resp1
    92 *-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1372</x><y>343</y><w>147</w><h>105</h></coordinates><panel_attributes>GraphNodeInfo
     92*-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1372</x><y>427</y><w>147</w><h>105</h></coordinates><panel_attributes>GraphNodeInfo
    9393--
    9494--
    … …  
    102102#GraphNodeInfo()
    103103#~GraphNodeInfo()
    104 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1484</x><y>525</y><w>126</w><h>70</h></coordinates><panel_attributes>GraphNode
     104</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1484</x><y>609</y><w>126</w><h>70</h></coordinates><panel_attributes>GraphNode
    105105--
    106106--
    … …  
    109109#OutputGraphInfo() const
    110110#OutputComponentNumber() const
    111 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1484</x><y>259</y><w>748</w><h>279</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>735;21;735;70;217;70;217;210;21;210;21;266</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1484</x><y>427</y><w>34</w><h>111</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;98</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1288</x><y>672</y><w>588</w><h>245</h></coordinates><panel_attributes>Atom
     111</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1484</x><y>343</y><w>748</w><h>279</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>735;21;735;70;217;70;217;210;21;210;21;266</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1484</x><y>511</y><w>34</w><h>111</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;98</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1288</x><y>756</y><w>588</w><h>245</h></coordinates><panel_attributes>Atom
    112112--
    113113sort: int*
    … …  
    129129#DistanceToVector(const Vector &amp;origin) const: double
    130130#DistanceSquaredToVector(const Vector &amp;origin) const: double
    131 #IsInParallelepiped(const Vector offset, const double *parallelepiped) const: bool</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1379</x><y>427</y><w>83</w><h>258</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;182;70;182;70;245</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2226</x><y>665</y><w>504</w><h>210</h></coordinates><panel_attributes>TrajectoryParticle
     131#IsInParallelepiped(const Vector offset, const double *parallelepiped) const: bool</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1379</x><y>511</y><w>83</w><h>258</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;182;70;182;70;245</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2226</x><y>749</y><w>504</w><h>210</h></coordinates><panel_attributes>TrajectoryParticle
    132132--
    133133--
    … …  
    147147#Thermostat_Berendsen(int Step, double ScaleTempFactor, double *ekin, config *configuration)
    148148#Thermostat_NoseHoover_init(int Step, double *delta_alpha)
    149 #Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration)</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2149</x><y>259</y><w>209</w><h>419</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;112;196;112;196;406</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1967</x><y>259</y><w>391</w><h>419</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;112;378;112;378;406</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1617</x><y>490</y><w>203</w><h>70</h></coordinates><panel_attributes>TrajectoryParticleInfo
     149#Thermostat_NoseHoover_scale(int Step, double *ekin, config *configuration)</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>2149</x><y>343</y><w>209</w><h>419</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;112;196;112;196;406</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1967</x><y>343</y><w>391</w><h>419</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;112;378;112;378;406</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1617</x><y>574</y><w>203</w><h>70</h></coordinates><panel_attributes>TrajectoryParticleInfo
    150150--
    151151Trajectory: struct {vector&lt;Vector&gt; R,U,V}
    … …  
    153153--
    154154#TrajectoryParticleInfo()
    155 #~TrajectoryParticleInfo()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1757</x><y>539</y><w>601</w><h>139</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;105;588;105;588;126</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>539</y><w>34</w><h>146</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;133</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1519</x><y>574</y><w>244</w><h>111</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;56;231;56;231;98</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1736</x><y>364</y><w>147</w><h>112</h></coordinates><panel_attributes>TesselPoint
     155#~TrajectoryParticleInfo()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1757</x><y>623</y><w>601</w><h>139</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;105;588;105;588;126</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>623</y><w>34</w><h>146</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;133</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1519</x><y>658</y><w>244</w><h>111</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>21;21;21;56;231;56;231;98</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1736</x><y>448</y><w>147</w><h>112</h></coordinates><panel_attributes>TesselPoint
    156156--
    157157-id: Long
    … …  
    163163Responsibilities
    164164-- Resp1
    165 *-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>455</y><w>146</w><h>230</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>133;21;133;175;21;175;21;217</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>588</y><w>398</w><h>97</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>385;21;385;42;21;42;21;84</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>259</y><w>398</w><h>426</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>385;21;385;168;196;168;196;371;21;371;21;413</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>259</y><w>209</w><h>426</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>196;21;196;371;21;371;21;413</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>833</x><y>770</y><w>357</w><h>224</h></coordinates><panel_attributes>Bond
     165*-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>539</y><w>146</w><h>230</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>133;21;133;175;21;175;21;217</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>672</y><w>398</w><h>97</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>385;21;385;42;21;42;21;84</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>343</y><w>398</w><h>426</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>385;21;385;168;196;168;196;371;21;371;21;413</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1729</x><y>343</y><w>209</w><h>426</h></coordinates><panel_attributes>lt=&lt;&lt;-</panel_attributes><additional_attributes>196;21;196;371;21;371;21;413</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>833</x><y>854</y><w>357</w><h>224</h></coordinates><panel_attributes>Bond
    166166--
    167167HydrogenBond: int
    … …  
    182182#bond()
    183183#bond(atom *left, atom *right, const int degree=1, const int number=0)
    184 #~bond()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1834</x><y>623</y><w>107</w><h>125</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    185 3</panel_attributes><additional_attributes>42;112;91;112;91;35;21;35;21;49</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1169</x><y>812</y><w>132</w><h>49</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    186 2</panel_attributes><additional_attributes>21;35;119;35</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>770</x><y>658</y><w>111</w><h>167</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    187 2</panel_attributes><additional_attributes>63;154;28;154;28;35;98;35;98;112</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1113</x><y>1246</y><w>504</w><h>168</h></coordinates><panel_attributes>BondGraph
     184#~bond()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1834</x><y>707</y><w>107</w><h>125</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     1853</panel_attributes><additional_attributes>42;112;91;112;91;35;21;35;21;49</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1169</x><y>896</y><w>132</w><h>49</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     1862</panel_attributes><additional_attributes>21;35;119;35</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>770</x><y>742</y><w>111</w><h>167</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     1872</panel_attributes><additional_attributes>63;154;28;154;28;35;98;35;98;112</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1113</x><y>1330</y><w>504</w><h>168</h></coordinates><panel_attributes>BondGraph
    188188--
    189189max_distance: double
    … …  
    199199                                                        double &amp;MinDistance, double &amp;MaxDistance, bool IsAngstroem)
    200200#CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker,
    201                                           double &amp;MinDistance, double &amp;MaxDistance, bool IsAngstroem)</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1596</x><y>1323</y><w>167</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;154;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1750</x><y>1281</y><w>147</w><h>133</h></coordinates><panel_attributes>MatrixContainer
     201                                          double &amp;MinDistance, double &amp;MaxDistance, bool IsAngstroem)</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1596</x><y>1407</y><w>167</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;154;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1750</x><y>1365</y><w>147</w><h>133</h></coordinates><panel_attributes>MatrixContainer
    202202--
    203203-id: Long
    … …  
    209209Responsibilities
    210210-- Resp1
    211 *-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>0</x><y>455</y><w>511</w><h>1050</h></coordinates><panel_attributes>config
     211*-- Resp2*</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>0</x><y>539</y><w>511</w><h>1050</h></coordinates><panel_attributes>config
    212212--
    213213PsiType: int
    … …  
    297297#SetDefaultPath(const char * const path);
    298298#InitThermostats();
    299 #ParseThermostats(class ConfigFileBuffer * const fb);</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>490</x><y>1344</y><w>636</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;623;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1596</x><y>0</y><w>121</w><h>139</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    300 2</panel_attributes><additional_attributes>70;126;105;126;105;35;21;35;21;63</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2520</x><y>896</y><w>224</w><h>140</h></coordinates><panel_attributes>&lt;&lt;Singleton&gt;&gt;
     299#ParseThermostats(class ConfigFileBuffer * const fb);</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>490</x><y>1428</y><w>636</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;623;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1596</x><y>84</y><w>121</w><h>139</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     3002</panel_attributes><additional_attributes>70;126;105;126;105;35;21;35;21;63</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2520</x><y>980</y><w>224</w><h>140</h></coordinates><panel_attributes>&lt;&lt;Singleton&gt;&gt;
    301301errorLogger
    302302--
    … …  
    310310#static setVerbosity(int verbosityLevel);
    311311#protected errorLogger()
    312 #protected ~errorLogger()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2093</x><y>980</y><w>364</w><h>35</h></coordinates><panel_attributes>KeyCompare
     312#protected ~errorLogger()</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>2093</x><y>1064</y><w>364</w><h>35</h></coordinates><panel_attributes>KeyCompare
    313313--
    314314--
    315315#operator() (const KeySet SubgraphA, const KeySet SubgraphB) const: bool
    316 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1169</x><y>1134</y><w>147</w><h>105</h></coordinates><panel_attributes>UniqueFragments
     316</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1169</x><y>1218</y><w>147</w><h>105</h></coordinates><panel_attributes>UniqueFragments
    317317--
    318318ANOVAOrder: int
    … …  
    322322ShortestPathList: int *
    323323UsedList: bool **
    324 BondsPerSPCount: int *</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>490</x><y>1169</y><w>692</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>679;21;21;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1120</x><y>896</y><w>251</w><h>307</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>49;294;21;294;21;224;238;224;238;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>840</x><y>1043</y><w>245</w><h>28</h></coordinates><panel_attributes>Graph
     324BondsPerSPCount: int *</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>490</x><y>1253</y><w>692</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>679;21;21;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1120</x><y>980</y><w>251</w><h>307</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>49;294;21;294;21;224;238;224;238;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>840</x><y>1127</y><w>245</w><h>28</h></coordinates><panel_attributes>Graph
    325325{map &lt;KeySet, NumberValuePair, KeyCompare&gt;}
    326 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>861</x><y>1050</y><w>321</w><h>153</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>308;140;21;140;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>945</x><y>1106</y><w>56</w><h>28</h></coordinates><panel_attributes>KeySet
    327 {set&lt;int&gt;}</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>945</x><y>1113</y><w>237</w><h>90</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>224;77;21;77;21;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1085</x><y>973</y><w>99</w><h>230</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
    328 0...N X 0...N</panel_attributes><additional_attributes>84;217;56;217;56;112;21;112;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1736</x><y>2198</y><w>147</w><h>42</h></coordinates><panel_attributes>LSQ_params
     326</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>861</x><y>1134</y><w>321</w><h>153</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>308;140;21;140;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>945</x><y>1190</y><w>56</w><h>28</h></coordinates><panel_attributes>KeySet
     327{set&lt;int&gt;}</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>945</x><y>1197</y><w>237</w><h>90</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>224;77;21;77;21;21</additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1085</x><y>1057</y><w>99</w><h>230</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-
     3280...N X 0...N</panel_attributes><additional_attributes>84;217;56;217;56;112;21;112;21;21</additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1736</x><y>2282</y><w>147</w><h>42</h></coordinates><panel_attributes>LSQ_params
    329329--
    330330vectors: const Vector **
    331331num: int
    332 </panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1043</x><y>182</y><w>147</w><h>35</h></coordinates><panel_attributes>lsq_params
    333 --
    334 x: gsl_vector *</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1169</x><y>182</y><w>118</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;105;21</additional_attributes></element></umlet_diagram>
     332</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Class</type><coordinates><x>1043</x><y>266</y><w>147</w><h>35</h></coordinates><panel_attributes>lsq_params
     333--
     334x: gsl_vector *</panel_attributes><additional_attributes></additional_attributes></element><element><type>com.umlet.element.base.Relation</type><coordinates><x>1169</x><y>266</y><w>118</w><h>34</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>21;21;105;21</additional_attributes></element></umlet_diagram>

  • src/Actions/Process.cpp

    rcd032d red58ad  
    3838
    3939int Process::getCurrStep(){
     40  OBSERVE;
    4041  return currStep;
    4142}
    4243
    4344void Process::setCurrStep(int _currStep){
    44   OBSERVE;
    4545  currStep = _currStep;
    4646}
    … …  
    5252    return 0;
    5353}
     54
    5455int Process::getMaxSteps(){
    5556  return maxSteps;

  • src/Actions/small_actions.hpp

    rcd032d red58ad  
    2525};
    2626
     27
    2728#endif // _SMALL_ACTIONS_HPP

  • src/Makefile.am

    rcd032d red58ad  
    88ANALYSISHEADER = analysis_bonds.hpp analysis_correlation.hpp
    99
    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.
    12 ACTIONSSOURCE = Actions/Action.cpp Actions/Process.cpp Actions/MethodAction.cpp Actions/ActionSequence.cpp Actions/MakroAction.cpp Actions/ManipulateAtomsProcess.cpp Actions/ActionRegistry.cpp
    13 ACTIONSHEADER = 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
    16 MENUACTIONSSOURCE = Actions/ErrorAction.cpp Actions/small_actions.cpp
    17 MENUACTIONSHEADER = Actions/ErrorAction.hpp Actions/small_actions.hpp
     10ACTIONSSOURCE = 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
     11ACTIONSHEADER = 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
    1812
    1913PATTERNSOURCE = Patterns/Observer.cpp
    … …  
    2822MENUHEADER = Menu/Menu.hpp Menu/TextMenu.hpp Menu/MenuItem.hpp Menu/SubMenuItem.hpp Menu/ActionMenuItem.hpp Menu/SeperatorItem.hpp Menu/DisplayMenuItem.hpp
    2923
    30 UISOURCE = ${MENUACTIONSSOURCE} ${VIEWSOURCE} ${MENUSOURCE} UIElements/TextUIFactory.cpp UIElements/MainWindow.cpp UIElements/TextWindow.cpp UIElements/Dialog.cpp UIElements/TextDialog.cpp UIElements/TextStatusIndicator.cpp
    31 UIHEADER = ${MENUACTIONSHEADER} ${VIEWHEADER} ${MENUHEADER} UIElements/TextUIFactory.hpp UIElements/MainWindow.hpp UIElements/TextWindow.hpp UIElements/Dialog.hpp UIElements/TextDialog.hpp UIElements/TextStatusIndicator.hpp
    32 
    33 FACTORYSOURCE = UIElements/UIFactory.cpp
    34 FACTORYHEADER = UIElements/UIFactory.hpp
     24UISOURCE = ${ACTIONSSOURCE} ${VIEWSOURCE} ${MENUSOURCE} UIElements/UIFactory.cpp UIElements/TextUIFactory.cpp UIElements/MainWindow.cpp UIElements/TextWindow.cpp UIElements/TextStatusIndicator.cpp UIElements/Dialog.cpp UIElements/TextDialog.cpp
     25UIHEADER = ${ACTIONSHEADER} ${VIEWHEADER} ${MENUHEADER} UIElements/UIFactory.hpp UIElements/TextUIFactory.hpp UIElements/MainWindow.hpp UIElements/TextWindow.hpp UIElements/TextStatusIndicator.hpp UIElements/Dialog.hpp UIElements/TextDialog.hpp
    3526
    3627# all these files are only used for legacy reasons while the transition is in progress
    … …  
    3930LEGACYSOURCE = Legacy/oldmenu.cpp
    4031LEGACYHEADER = Legacy/oldmenu.hpp
    41 
    42 QTUIMOC_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  
    50 QTUIMOC_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
    5732
    5833DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
    … …  
    6843                                   Descriptors/MoleculeIdDescriptor.hpp
    6944
    70 QTUISOURCE = ${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              
    80 QTUIHEADER = ${QTUIMOC_HEADER} UIElements/QT4/QTUIFactory.hpp
    81 
    82 QTUI_DEFS =
    83 
    84 SOURCE = ${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
    85 HEADER = ${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
     45SOURCE = ${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
     46HEADER = ${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
    8647
    8748BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
    88 GUI_LIBS = ${QT_LDADD} ${QT_LIB_GUI} -lQtOpenGL ${GLU_LIBS}
    8949INCLUDES = -I$(top_srcdir)/src/unittests
    9050
    91 noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a libmenu.a
    92 bin_PROGRAMS = molecuilder molecuildergui joiner analyzer
     51noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a
     52bin_PROGRAMS = molecuilder joiner analyzer
    9353molecuilderdir = ${bindir}
    94 
    9554libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
    96 
    97 libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER}
    98 
    9955libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
    100 
    10156molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
    102 
    103 molecuilder_CXXFLAGS = $(BOOST_CPPFLAGS)
    104 #molecuilder_CXXFLAGS += -DNO_CACHING
    105 molecuilder_LDFLAGS = $(BOOST_LIB)
    106 molecuilder_SOURCES = ${FACTORYSOURCE} ${LEGACYSOURCE} builder.cpp
    107 molecuilder_SOURCES += $(srcdir)/version.c
    108 molecuilder_LDADD = libmolecuilder.a libgslwrapper.a libmenu.a ${BOOST_THREAD_LIB}
    109 
    110 #Stuff for building the GUI using QT
    111 molecuildergui_SOURCES = ${QTUISOURCE} ${FACTORYSOURCE} ${LEGACYSOURCE} builder.cpp
    112 molecuildergui_SOURCES += $(srcdir)/version.c
    113 molecuildergui_CXXFLAGS = ${QT_CXXFLAGS} ${GLU_CXXFLAGS} -DUSE_GUI_QT
    114 molecuildergui_LDFLAGS = $(BOOST_LIB) ${QT_LDFLAGS} ${GLU_LDFLAGS}
    115 molecuildergui_LDADD = libmolecuilder.a libgslwrapper.a libmenu.a ${BOOST_THREAD_LIB} ${GUI_LIBS}
    116 
     57molecuilder_LDFLAGS = $(BOOST_LDFLAGS)
     58molecuilder_SOURCES = builder.cpp
     59molecuilder_LDADD = libmolecuilder.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    11760joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
    11861joiner_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    119 
    12062analyzer_SOURCES = analyzer.cpp datacreator.cpp parser.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp
    12163analyzer_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    12264
    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 
    135 MOSTLYCLEANFILES = ${QTUIMOC_TARGETS}
    136        
    13765#EXTRA_DIST = ${molecuilder_DATA}
    13866
    … …  
    15179        echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
    15280
    153 
     81molecuilder_SOURCES += $(srcdir)/version.c

  • src/UIElements/Dialog.cpp

    rcd032d red58ad  
    3131
    3232bool Dialog::display(){
    33   if(checkAll()){
    34     setAll();
    35     return true;
    36   }
    37   else{
    38     return false;
    39   }
    40 }
    41 
    42 bool Dialog::checkAll(){
    4333  list<Query*>::iterator iter;
    4434  bool retval = true;
    … …  
    4939      break;
    5040  }
     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    }
     46  }
    5147  return retval;
    52 }
    53 
    54 void Dialog::setAll(){
    55   list<Query*>::iterator iter;
    56   for(iter=queries.begin(); iter!=queries.end(); iter++) {
    57     (*iter)->setResult();
    58   }
    5948}
    6049
    … …  
    8776
    8877Dialog::StringQuery::StringQuery(string title,string *_target) :
    89     Query(title),
    90     target(_target),
    91     tmp("")
     78    Query(title), target(_target)
    9279{}
    9380
    … …  
    146133  *target = *tmp;
    147134}
    148 
    149 // Element Queries
    150 Dialog::ElementQuery::ElementQuery(std::string title, element **_target) :
    151   Query(title),
    152   target(_target),
    153   tmp(0)
    154   {}
    155 
    156 Dialog::ElementQuery::~ElementQuery(){}
    157 
    158 void Dialog::ElementQuery::setResult(){
    159   *target=tmp;
    160 }

  • src/UIElements/Dialog.hpp

    rcd032d red58ad  
    1515class molecule;
    1616class Vector;
    17 class element;
    1817
    1918class Dialog
    … …  
    2827  virtual void queryMolecule(const char*,molecule**,MoleculeListClass*)=0;
    2928  virtual void queryVector(const char*,Vector *,const double *const,bool)=0;
    30   virtual void queryElement(const char*,element **)=0;
    3129
    3230  virtual bool display();
    33 
    34   virtual bool checkAll();
    35   virtual void setAll();
    3631
    3732protected:
    … …  
    5045  public:
    5146    Query(std::string _title);
    52     virtual ~Query();
     47    ~Query();
    5348    virtual bool handle()=0;
    5449    virtual void setResult()=0;
    … …  
    6358  public:
    6459    IntQuery(std::string title,int *_target);
    65     virtual ~IntQuery();
     60    ~IntQuery();
    6661    virtual bool handle()=0;
    6762    virtual void setResult();
    … …  
    7570  public:
    7671    DoubleQuery(std::string title,double *_target);
    77     virtual ~DoubleQuery();
     72    ~DoubleQuery();
    7873    virtual bool handle()=0;
    7974    virtual void setResult();
    … …  
    8782  public:
    8883    StringQuery(std::string title,std::string *_target);
    89     virtual ~StringQuery();
     84    ~StringQuery();
    9085    virtual bool handle()=0;
    9186    virtual void setResult();
    … …  
    10095  public:
    10196    MoleculeQuery(std::string title, molecule **_target, MoleculeListClass *_molecules);
    102     virtual ~MoleculeQuery();
     97    ~MoleculeQuery();
    10398    virtual bool handle()=0;
    10499    virtual void setResult();
    … …  
    113108  public:
    114109      VectorQuery(std::string title,Vector *_target,const double *const _cellSize,bool _check);
    115       virtual ~VectorQuery();
     110      ~VectorQuery();
    116111      virtual bool handle()=0;
    117112      virtual void setResult();
    … …  
    124119  };
    125120
    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 
    138121void registerQuery(Query* query);
    139122

  • src/UIElements/TextDialog.cpp

    rcd032d red58ad  
    1010#include "UIElements/TextDialog.hpp"
    1111
    12 #include "World.hpp"
    13 #include "periodentafel.hpp"
    1412#include "atom.hpp"
    1513#include "molecule.hpp"
    … …  
    4745void TextDialog::queryVector(const char* title, Vector *target,const double *const cellSize, bool check) {
    4846  registerQuery(new VectorTextQuery(title,target,cellSize,check));
    49 }
    50 
    51 void TextDialog::queryElement(const char* title, element **target){
    52   registerQuery(new ElementTextQuery(title,target));
    5347}
    5448
    … …  
    119113
    120114bool TextDialog::VectorTextQuery::handle() {
    121  Log() << Verbose(0) << getTitle();
    122115 tmp->AskPosition(cellSize,check);
    123116 return true;
    124117}
    125 
    126 
    127 TextDialog::ElementTextQuery::ElementTextQuery(std::string title, element **target) :
    128     Dialog::ElementQuery(title,target)
    129 {}
    130 
    131 TextDialog::ElementTextQuery::~ElementTextQuery()
    132 {}
    133 
    134 bool 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

    rcd032d red58ad  
    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 **);
    2726
    2827protected:
    … …  
    3130  public:
    3231    IntTextQuery(std::string title, int *_target);
    33     virtual ~IntTextQuery();
     32    ~IntTextQuery();
    3433    virtual bool handle();
    3534  };
    … …  
    3837  public:
    3938    DoubleTextQuery(std::string title, double *_target);
    40     virtual ~DoubleTextQuery();
     39    ~DoubleTextQuery();
    4140    virtual bool handle();
    4241  };
    … …  
    4544  public:
    4645    StringTextQuery(std::string title, std::string *_target);
    47     virtual ~StringTextQuery();
     46    ~StringTextQuery();
    4847    virtual bool handle();
    4948  };
    … …  
    5251  public:
    5352    MoleculeTextQuery(std::string title, molecule **_target, MoleculeListClass *_molecules);
    54     virtual ~MoleculeTextQuery();
     53    ~MoleculeTextQuery();
    5554    virtual bool handle();
    5655  };
    … …  
    5958  public:
    6059    VectorTextQuery(std::string title,Vector *_target,const double *const _cellSize,bool _check);
    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();
     60    ~VectorTextQuery();
    6961    virtual bool handle();
    7062  };

  • src/UIElements/TextUIFactory.hpp

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

  • src/UIElements/UIFactory.cpp

    rcd032d red58ad  
    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
    1815
    1916UIFactory::UIFactory()
    … …  
    3330      setInstance(new TextUIFactory());
    3431      break;
    35 #ifdef USE_GUI_QT
    36     case QT4 :
    37       setInstance(new QTUIFactory());
    38       break;
    39 #endif
     32
    4033    default:
    4134      assert(0 && "No such Factory in stock");

  • src/UIElements/UIFactory.hpp

    rcd032d red58ad  
    3131
    3232public:
    33   enum InterfaceTypes {
    34     Text,
    35 #ifdef USE_GUI_QT
    36     QT4
    37 #endif
    38 };
     33  enum InterfaceTypes {Text};
    3934  virtual ~UIFactory();
    4035

  • src/builder.cpp

    rcd032d red58ad  
    451451  mol->Mirror((const Vector *)&n);
    452452};
    453 >>>>>>> MenuRefactoring:molecuilder/src/builder.cpp
    454453
    455454/** Submenu for removing the atoms from the molecule.
    … …  
    22062205        mol = World::getInstance().createMolecule();
    22072206        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
    22192221      setVerbosity(0);
    22202222
    … …  
    22222224      populaters.MakeEditMoleculesMenu = populateEditMoleculesMenu;
    22232225
    2224 #ifdef USE_GUI_QT
    2225       UIFactory::makeUserInterface(UIFactory::QT4);
    2226 #else
    2227       cout << ESPACKVersion << endl;
    22282226      UIFactory::makeUserInterface(UIFactory::Text);
    2229 #endif
    22302227      MainWindow *mainWindow = UIFactory::getInstance().makeMainWindow(populaters,World::getInstance().getMolecules(), configuration, World::getInstance().getPeriode(), ConfigFileName);
    22312228      mainWindow->display();
    2232 
    22332229      delete mainWindow;
    22342230    }

  • src/defs.hpp

    rcd032d red58ad  
    8585#define STD_SEPERATOR_SPACER '-'
    8686
    87 #define MOLECUILDER_NAME "Molecuilder"
     87// some types used to set template parameters
     88struct true_type{
     89  enum{value=1};
     90};
     91struct false_type{
     92  enum{value = 0};
     93};
    8894
    8995#endif /*DEFS_HPP_*/

  • src/unittests/Makefile.am

    rcd032d red58ad  
    44AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
    55
    6 MENUTESTS = ActionSequenceTest
    7 
     6MENUTESTS = ActionSequenceTest
    87
    98TESTS = \
    … …  
    3736  ${MENUTESTS}
    3837 
    39  
     38
     39     
     40 
    4041check_PROGRAMS = $(TESTS)
    4142noinst_PROGRAMS = $(TESTS) TestRunner

  • src/vector.cpp

    rcd032d red58ad  
    2020#include <gsl/gsl_permutation.h>
    2121#include <gsl/gsl_vector.h>
    22 
    23 #include <cassert>
    2422
    2523/************************************ Functions for class vector ************************************/
    … …  
    661659  return x;
    662660};
    663 
    664 Vector& Vector::operator=(const Vector& src) {
    665   CopyVector(src);
    666   return *this;
    667 }
    668 
    669 double& Vector::operator[](int i){
    670   assert(i<NDIM && "Invalid Vector dimension requested");
    671   return x[i];
    672 }
    673661
    674662/** Prints a 3dim vector.

  • src/vector.hpp

    rcd032d red58ad  
    8080  void WrapPeriodically(const double * const M, const double * const Minv);
    8181
    82   Vector& operator=(const Vector &src);
    83   double& operator[](int i);
    84 
    8582};
    8683
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