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Molby: コミット

Molecular Modeling Software

コミットメタ情報

リビジョン	1cfe36ca707ed98020a1dbdb035935c3dc937885 (tree)
日時	2014-03-27 10:10:17
作者	toshinagata1964 <toshinagata1964@a2be...>
コミッター	toshinagata1964

ログメッセージ

Embedded Ruby: problems with encoding is being fixed (not complete yet?)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@513 a2be9bc6-48de-4e38-9406-05402d4bc13c

変更サマリ

modified: Documents/src/doc_source.html (diff)
modified: Makefile (diff)
modified: MolLib/Ruby_bind/Molby_extern.h (diff)
modified: MolLib/Ruby_bind/ruby_bind.c (diff)
modified: Scripts/crystal.rb (diff)
modified: Scripts/gamess.rb (diff)
modified: Scripts/startup.rb (diff)
modified: Scripts/view.rb (diff)
modified: how_to_build (diff)
modified: wxSources/ConsoleFrame.cpp (diff)
modified: wxSources/MyApp.cpp (diff)
modified: xcode-build/Molby.xcodeproj/project.pbxproj (diff)

差分

--- a/Documents/src/doc_source.html

+++ b/Documents/src/doc_source.html

		@@ -935,9 +935,6 @@ The parameter table shows the molecular mechanics parameters in one table.
935	935	</p>
936	936	<p><img src="../etc/table_12.png" /></p>
937	937	<p>
938		-When you build a molecule from scratch, and open the parameter table before doing any MM/MD operations, this table is likely to be empty. This is because the MM parameters are looked up only when "Molecular Dynamics..." or "Minimize..." menu command is invoked, or you use MM/MD tools like Antechamber (see Step 4 for details). After doing some of these operations, you will see a set of parameters shown in this table.
939		-</p>
940		-<p>
941	938	The parameters are grouped in several classes, namely "VDWs", "Bonds", "Angles", "Dihedrals", "Impropers", and "VDW Pairs".
942	939	</p>
943	940	<p>

		@@ -1028,9 +1025,6 @@ Bond, angle, dihedral, improper テーブルは、それぞれ結合・結合角
1028	1025	</p>
1029	1026	<p><img src="../etc/table_12.png" /></p>
1030	1027	<p>
1031		-分子を新しく作成して、MM/MD に関連する操作を何もせずにパラメータテーブルを開くと、テーブルはおそらく空のままでしょう。分子力学パラメータは、"Molecular Dynamics..." または "Minimize..." メニューコマンドを実行したときか、Antechamber のような分子力学用ツール（第四段階参照）を使った時に初めて作成されます。これらの操作をした後には、パラメータがこのテーブルに表示されます。
1032		-</p>
1033		-<p>
1034	1028	パラメータはいくつかの種類にグループ分けされています。"VDWs", "Bonds", "Angles", "Dihedrals", "Impropers", そして "VDW Pairs" です。
1035	1029	</p>
1036	1030	<p>

		@@ -1099,7 +1093,7 @@ Open the "MM/MD" menu, and select "Guess MM/MD Parameters..." command.
1099	1093	</p>
1100	1094	<p><img src="../etc/minimize_02.png" /></p>
1101	1095	<p>
1102		-A dialog like below shows up. This is for execution of Antechamber on the current molecule. Turn off the "partial charge" checkbox. The "log" directory is used by AmberTools for storing intermediate files; the default value would be acceptable, but you can change it here.
	1096	+A dialog like below shows up. This is for execution of Antechamber on the current molecule. Turn off the "Calculate partial charges" checkbox, and turn on the "Guess atom types" checkbox. The "log" directory is used by AmberTools for storing intermediate files; the default value would be acceptable, but you can change it here.
1103	1097	</p>
1104	1098	<p><img src="../etc/minimize_03.png" /></p>
1105	1099	<p>

		@@ -1188,7 +1182,7 @@ Molby の分子力学計算は、基本的な分子力場（結合の伸縮、
1188	1182	</p>
1189	1183	<p><img src="../etc/minimize_02.png" /></p>
1190	1184	<p>
1191		-下のようなダイアログが現れます。これは現在の分子に対して Antechamber を実行するためのものです。一番上のチェックボックス (partial charge) をオフにしてください。"Log" ディレクトリは、AmberTools のプログラムが中間ファイルを保存するのに使います。デフォルトの位置で問題はないでしょうが、変更してもかまいません。
	1185	+下のようなダイアログが現れます。これは現在の分子に対して Antechamber を実行するためのものです。一番上のチェックボックス "Calculate partial charge" をオフ、その下の "Guess Atom Types" をオンにしてください。"Log" ディレクトリは、AmberTools のプログラムが中間ファイルを保存するのに使います。デフォルトの位置で問題はないでしょうが、変更してもかまいません。
1192	1186	</p>
1193	1187	<p><img src="../etc/minimize_03.png" /></p>
1194	1188	<p>

--- a/Makefile

+++ b/Makefile

		@@ -8,7 +8,7 @@ ifeq ($(TARGET_PLATFORM),MAC)
8	8	LD_EXTRA_FLAGS = -framework Accelerate -framework GLUT -L$(PWD)/../../fftw-3.3.2/osx-build/lib -lfftw3
9	9	RUBY_DIR = $(PWD)/../../ruby-1.8.7-p160
10	10	RUBY_CFLAGS = -isystem $(RUBY_DIR)/osx-build/include
11		- RUBY_LDFLAGS = -L$(RUBY_DIR)/osx-build/lib -lruby-static
	11	+ RUBY_LDFLAGS = -L$(RUBY_DIR)/osx-build/lib -lruby-static -lenc
12	12	EXECUTABLE = Molby
13	13	EXE_SUFFIX =
14	14	endif

		@@ -23,7 +23,7 @@ ifeq ($(TARGET_PLATFORM),MSW)
23	23	LD_EXTRA_FLAGS = -L$(PWD)/../../CLAPACK-3.1.1.1-mingw/lib -L$(PWD)/../../fftw-3.3.2/msw-build/lib -llapackMinGW -lblasMinGW -lf2c_nomain -lfftw3
24	24	RUBY_DIR = $(PWD)/../../ruby-2.0.0-p353
25	25	RUBY_CFLAGS = -isystem $(RUBY_DIR)/msw-build/include/ruby-2.0.0 -I$(RUBY_DIR) -I$(RUBY_DIR)/msw-build/include/ruby-2.0.0/i386-mingw32
26		- RUBY_LDFLAGS = -L$(RUBY_DIR)/msw-build/lib -lmsvcrt-ruby200-static -lmsvcrt-ruby200 -lws2_32 -lshlwapi -limagehlp
	26	+ RUBY_LDFLAGS = -L$(RUBY_DIR)/msw-build/lib -lmsvcrt-ruby200-static -lmsvcrt-ruby200 -lws2_32 -lshlwapi -limagehlp -lenc
27	27	EXECUTABLE = _Molby.exe_
28	28	FINAL_EXECUTABLE = Molby.exe
29	29	EXE_SUFFIX = .exe

--- a/MolLib/Ruby_bind/Molby_extern.h

+++ b/MolLib/Ruby_bind/Molby_extern.h

		@@ -37,7 +37,7 @@ extern void Molby_showError(int status);
37	37	extern RubyValue Molby_evalRubyScriptOnMolecule(const char script, Molecule mol, const char fname, int status);
38	38	/* extern RubyValue Molby_evalRubyScript(const char script, int status);
39	39	extern RubyValue Molby_evalRubyScriptOnActiveMoleculeWithInterrupt(const char script, int status); */
40		-extern void Molby_showRubyValue(RubyValue value, char **outValueString);
	40	+extern int Molby_showRubyValue(RubyValue value, char **outValueString);
41	41	extern int Ruby_UpdateUI(int index, Molecule mol, int outChecked, char **outTitle);
42	42	/extern int Ruby_methodType(const char className, const char methodName);/
43	43	extern void Molby_buildARGV(int argc, const char **argv);

--- a/MolLib/Ruby_bind/ruby_bind.c

+++ b/MolLib/Ruby_bind/ruby_bind.c

		@@ -11065,7 +11065,11 @@ s_evalRubyScriptOnMoleculeSub(VALUE val)
11065	11065	if (ptr[2] == NULL) {
11066	11066	char *scr;
11067	11067	/* String literal: we need to specify string encoding */
	11068	+#if defined(__WXMSW__)
	11069	+ asprintf(&scr, "#coding:shift_jis\n%s", (char *)ptr[0]);
	11070	+#else
11068	11071	asprintf(&scr, "#coding:utf-8\n%s", (char *)ptr[0]);
	11072	+#endif
11069	11073	sval = rb_str_new2(scr);
11070	11074	free(scr);
11071	11075	fnval = rb_str_new2("(eval)");

		@@ -11124,13 +11128,13 @@ Molby_evalRubyScriptOnMolecule(const char script, Molecule mol, const char *fn
11124	11128	return retval;
11125	11129	}
11126	11130
11127		-void
	11131	+int
11128	11132	Molby_showRubyValue(RubyValue value, char **outValueString)
11129	11133	{
11130	11134	VALUE val = (VALUE)value;
11131	11135	if (gMolbyIsCheckingInterrupt) {
11132	11136	MolActionAlertRubyIsRunning();
11133		- return;
	11137	+ return 0;
11134	11138	}
11135	11139	if (val != Qnil) {
11136	11140	int status;

		@@ -11138,11 +11142,17 @@ Molby_showRubyValue(RubyValue value, char **outValueString)
11138	11142	gMolbyRunLevel++;
11139	11143	val = rb_protect(rb_inspect, val, &status);
11140	11144	gMolbyRunLevel--;
	11145	+ if (status != 0)
	11146	+ return status;
11141	11147	str = StringValuePtr(val);
11142	11148	if (outValueString != NULL)
11143	11149	*outValueString = strdup(str);
11144	11150	MyAppCallback_showScriptMessage("%s", str);
	11151	+ } else {
	11152	+ if (outValueString != NULL)
	11153	+ *outValueString = NULL;
11145	11154	}
	11155	+ return 0;
11146	11156	}
11147	11157
11148	11158	void

		@@ -11301,6 +11311,11 @@ Molby_startup(const char script, const char dir)
11301	11311	}
11302	11312	#endif
11303	11313	ruby_init();
	11314	+
	11315	+ {
	11316	+ extern void Init_shift_jis(void);
	11317	+ Init_shift_jis();
	11318	+ }
11304	11319
11305	11320	/* Initialize loadpath; the specified directory, "lib" subdirectory, and "." */
11306	11321	ruby_incpush(".");

--- a/Scripts/crystal.rb

+++ b/Scripts/crystal.rb

		@@ -1,4 +1,5 @@
1		-#
	1	+# coding: utf-8
	2	+#
2	3	# crystal.rb
3	4	#
4	5	# Created by Toshi Nagata.

		@@ -1807,7 +1808,8 @@ end
1807	1808	new_box = nil
1808	1809	hash = Dialog.run("Unit Cell") {
1809	1810	@mol = mol
1810		- @box = @mol.box.dup
	1811	+ @box = @mol.box
	1812	+ @box = (@box ? @box.dup : nil)
1811	1813	@box_save = nil
1812	1814
1813	1815	def set_cell_value(item1)

--- a/Scripts/gamess.rb

+++ b/Scripts/gamess.rb

		@@ -195,7 +195,12 @@ class Molecule
195	195	fpout.print freebytes
196	196
197	197	# Copy the input file
198		- scrprefix = scrdir + sep + inpbody
	198	+ scrprefix = scrdir + sep + inpbody
	199	+ if $platform == "win"
	200	+ scrbody = inpbody
	201	+ else
	202	+ scrbody = scrprefix
	203	+ end
199	204	filecopy(inpname, scrprefix + ".F05")
200	205
201	206	# Prepare environmental variables

		@@ -205,140 +210,140 @@ class Molecule
205	210	ENV["BASPATH"] = "#{auxdir}#{sep}BASES"
206	211	ENV["QUANPOL"] = "#{auxdir}#{sep}QUANPOL"
207	212	ENV["EXTBAS"] = "/dev/null"
208		- ENV["IRCDATA"] = "#{scrprefix}.irc"
209		- ENV["PUNCH"] = "#{scrprefix}.dat"
210		- ENV["INPUT"] = "#{scrprefix}.F05"
211		- ENV["AOINTS"] = "#{scrprefix}.F08"
212		- ENV["MOINTS"] = "#{scrprefix}.F09"
213		- ENV["DICTNRY"] = "#{scrprefix}.F10"
214		- ENV["DRTFILE"] = "#{scrprefix}.F11"
215		- ENV["CIVECTR"] = "#{scrprefix}.F12"
216		- ENV["CASINTS"] = "#{scrprefix}.F13"
217		- ENV["CIINTS"] = "#{scrprefix}.F14"
218		- ENV["WORK15"] = "#{scrprefix}.F15"
219		- ENV["WORK16"] = "#{scrprefix}.F16"
220		- ENV["CSFSAVE"] = "#{scrprefix}.F17"
221		- ENV["FOCKDER"] = "#{scrprefix}.F18"
222		- ENV["WORK19"] = "#{scrprefix}.F19"
223		- ENV["DASORT"] = "#{scrprefix}.F20"
224		- ENV["DFTINTS"] = "#{scrprefix}.F21"
225		- ENV["DFTGRID"] = "#{scrprefix}.F22"
226		- ENV["JKFILE"] = "#{scrprefix}.F23"
227		- ENV["ORDINT"] = "#{scrprefix}.F24"
228		- ENV["EFPIND"] = "#{scrprefix}.F25"
229		- ENV["PCMDATA"] = "#{scrprefix}.F26"
230		- ENV["PCMINTS"] = "#{scrprefix}.F27"
231		- ENV["MLTPL"] = "#{scrprefix}.F28"
232		- ENV["MLTPLT"] = "#{scrprefix}.F29"
233		- ENV["DAFL30"] = "#{scrprefix}.F30"
234		- ENV["SOINTX"] = "#{scrprefix}.F31"
235		- ENV["SOINTY"] = "#{scrprefix}.F32"
236		- ENV["SOINTZ"] = "#{scrprefix}.F33"
237		- ENV["SORESC"] = "#{scrprefix}.F34"
238		- ENV["SIMEN"] = "#{scrprefix}.simen"
239		- ENV["SIMCOR"] = "#{scrprefix}.simcor"
240		- ENV["GCILIST"] = "#{scrprefix}.F37"
241		- ENV["HESSIAN"] = "#{scrprefix}.F38"
242		- ENV["SOCCDAT"] = "#{scrprefix}.F40"
243		- ENV["AABB41"] = "#{scrprefix}.F41"
244		- ENV["BBAA42"] = "#{scrprefix}.F42"
245		- ENV["BBBB43"] = "#{scrprefix}.F43"
246		- ENV["MCQD50"] = "#{scrprefix}.F50"
247		- ENV["MCQD51"] = "#{scrprefix}.F51"
248		- ENV["MCQD52"] = "#{scrprefix}.F52"
249		- ENV["MCQD53"] = "#{scrprefix}.F53"
250		- ENV["MCQD54"] = "#{scrprefix}.F54"
251		- ENV["MCQD55"] = "#{scrprefix}.F55"
252		- ENV["MCQD56"] = "#{scrprefix}.F56"
253		- ENV["MCQD57"] = "#{scrprefix}.F57"
254		- ENV["MCQD58"] = "#{scrprefix}.F58"
255		- ENV["MCQD59"] = "#{scrprefix}.F59"
256		- ENV["MCQD60"] = "#{scrprefix}.F60"
257		- ENV["MCQD61"] = "#{scrprefix}.F61"
258		- ENV["MCQD62"] = "#{scrprefix}.F62"
259		- ENV["MCQD63"] = "#{scrprefix}.F63"
260		- ENV["MCQD64"] = "#{scrprefix}.F64"
261		- ENV["NMRINT1"] = "#{scrprefix}.F61"
262		- ENV["NMRINT2"] = "#{scrprefix}.F62"
263		- ENV["NMRINT3"] = "#{scrprefix}.F63"
264		- ENV["NMRINT4"] = "#{scrprefix}.F64"
265		- ENV["NMRINT5"] = "#{scrprefix}.F65"
266		- ENV["NMRINT6"] = "#{scrprefix}.F66"
267		- ENV["DCPHFH2"] = "#{scrprefix}.F67"
268		- ENV["DCPHF21"] = "#{scrprefix}.F68"
269		- ENV["GVVPT"] = "#{scrprefix}.F69"
	213	+ ENV["IRCDATA"] = "#{scrbody}.irc"
	214	+ ENV["PUNCH"] = "#{scrbody}.dat"
	215	+ ENV["INPUT"] = "#{scrbody}.F05"
	216	+ ENV["AOINTS"] = "#{scrbody}.F08"
	217	+ ENV["MOINTS"] = "#{scrbody}.F09"
	218	+ ENV["DICTNRY"] = "#{scrbody}.F10"
	219	+ ENV["DRTFILE"] = "#{scrbody}.F11"
	220	+ ENV["CIVECTR"] = "#{scrbody}.F12"
	221	+ ENV["CASINTS"] = "#{scrbody}.F13"
	222	+ ENV["CIINTS"] = "#{scrbody}.F14"
	223	+ ENV["WORK15"] = "#{scrbody}.F15"
	224	+ ENV["WORK16"] = "#{scrbody}.F16"
	225	+ ENV["CSFSAVE"] = "#{scrbody}.F17"
	226	+ ENV["FOCKDER"] = "#{scrbody}.F18"
	227	+ ENV["WORK19"] = "#{scrbody}.F19"
	228	+ ENV["DASORT"] = "#{scrbody}.F20"
	229	+ ENV["DFTINTS"] = "#{scrbody}.F21"
	230	+ ENV["DFTGRID"] = "#{scrbody}.F22"
	231	+ ENV["JKFILE"] = "#{scrbody}.F23"
	232	+ ENV["ORDINT"] = "#{scrbody}.F24"
	233	+ ENV["EFPIND"] = "#{scrbody}.F25"
	234	+ ENV["PCMDATA"] = "#{scrbody}.F26"
	235	+ ENV["PCMINTS"] = "#{scrbody}.F27"
	236	+ ENV["MLTPL"] = "#{scrbody}.F28"
	237	+ ENV["MLTPLT"] = "#{scrbody}.F29"
	238	+ ENV["DAFL30"] = "#{scrbody}.F30"
	239	+ ENV["SOINTX"] = "#{scrbody}.F31"
	240	+ ENV["SOINTY"] = "#{scrbody}.F32"
	241	+ ENV["SOINTZ"] = "#{scrbody}.F33"
	242	+ ENV["SORESC"] = "#{scrbody}.F34"
	243	+ ENV["SIMEN"] = "#{scrbody}.simen"
	244	+ ENV["SIMCOR"] = "#{scrbody}.simcor"
	245	+ ENV["GCILIST"] = "#{scrbody}.F37"
	246	+ ENV["HESSIAN"] = "#{scrbody}.F38"
	247	+ ENV["SOCCDAT"] = "#{scrbody}.F40"
	248	+ ENV["AABB41"] = "#{scrbody}.F41"
	249	+ ENV["BBAA42"] = "#{scrbody}.F42"
	250	+ ENV["BBBB43"] = "#{scrbody}.F43"
	251	+ ENV["MCQD50"] = "#{scrbody}.F50"
	252	+ ENV["MCQD51"] = "#{scrbody}.F51"
	253	+ ENV["MCQD52"] = "#{scrbody}.F52"
	254	+ ENV["MCQD53"] = "#{scrbody}.F53"
	255	+ ENV["MCQD54"] = "#{scrbody}.F54"
	256	+ ENV["MCQD55"] = "#{scrbody}.F55"
	257	+ ENV["MCQD56"] = "#{scrbody}.F56"
	258	+ ENV["MCQD57"] = "#{scrbody}.F57"
	259	+ ENV["MCQD58"] = "#{scrbody}.F58"
	260	+ ENV["MCQD59"] = "#{scrbody}.F59"
	261	+ ENV["MCQD60"] = "#{scrbody}.F60"
	262	+ ENV["MCQD61"] = "#{scrbody}.F61"
	263	+ ENV["MCQD62"] = "#{scrbody}.F62"
	264	+ ENV["MCQD63"] = "#{scrbody}.F63"
	265	+ ENV["MCQD64"] = "#{scrbody}.F64"
	266	+ ENV["NMRINT1"] = "#{scrbody}.F61"
	267	+ ENV["NMRINT2"] = "#{scrbody}.F62"
	268	+ ENV["NMRINT3"] = "#{scrbody}.F63"
	269	+ ENV["NMRINT4"] = "#{scrbody}.F64"
	270	+ ENV["NMRINT5"] = "#{scrbody}.F65"
	271	+ ENV["NMRINT6"] = "#{scrbody}.F66"
	272	+ ENV["DCPHFH2"] = "#{scrbody}.F67"
	273	+ ENV["DCPHF21"] = "#{scrbody}.F68"
	274	+ ENV["GVVPT"] = "#{scrbody}.F69"
270	275
271	276	# next files are used only during coupled cluster runs, so let's
272	277	# display the numerous definitions only if they are to be used.
273		- ENV["CCREST"] = "#{scrprefix}.F70"
274		- ENV["CCDIIS"] = "#{scrprefix}.F71"
275		- ENV["CCINTS"] = "#{scrprefix}.F72"
276		- ENV["CCT1AMP"] = "#{scrprefix}.F73"
277		- ENV["CCT2AMP"] = "#{scrprefix}.F74"
278		- ENV["CCT3AMP"] = "#{scrprefix}.F75"
279		- ENV["CCVM"] = "#{scrprefix}.F76"
280		- ENV["CCVE"] = "#{scrprefix}.F77"
281		- ENV["EOMSTAR"] = "#{scrprefix}.F80"
282		- ENV["EOMVEC1"] = "#{scrprefix}.F81"
283		- ENV["EOMVEC2"] = "#{scrprefix}.F82"
284		- ENV["EOMHC1"] = "#{scrprefix}.F83"
285		- ENV["EOMHC2"] = "#{scrprefix}.F84"
286		- ENV["EOMHHHH"] = "#{scrprefix}.F85"
287		- ENV["EOMPPPP"] = "#{scrprefix}.F86"
288		- ENV["EOMRAMP"] = "#{scrprefix}.F87"
289		- ENV["EOMRTMP"] = "#{scrprefix}.F88"
290		- ENV["EOMDG12"] = "#{scrprefix}.F89"
291		- ENV["MMPP"] = "#{scrprefix}.F90"
292		- ENV["MMHPP"] = "#{scrprefix}.F91"
293		- ENV["MMCIVEC"] = "#{scrprefix}.F92"
294		- ENV["MMCIVC1"] = "#{scrprefix}.F93"
295		- ENV["MMCIITR"] = "#{scrprefix}.F94"
296		- ENV["MMNEXM"] = "#{scrprefix}.F95"
297		- ENV["MMNEXE"] = "#{scrprefix}.F96"
298		- ENV["MMNREXM"] = "#{scrprefix}.F97"
299		- ENV["MMNREXE"] = "#{scrprefix}.F98 "
	278	+ ENV["CCREST"] = "#{scrbody}.F70"
	279	+ ENV["CCDIIS"] = "#{scrbody}.F71"
	280	+ ENV["CCINTS"] = "#{scrbody}.F72"
	281	+ ENV["CCT1AMP"] = "#{scrbody}.F73"
	282	+ ENV["CCT2AMP"] = "#{scrbody}.F74"
	283	+ ENV["CCT3AMP"] = "#{scrbody}.F75"
	284	+ ENV["CCVM"] = "#{scrbody}.F76"
	285	+ ENV["CCVE"] = "#{scrbody}.F77"
	286	+ ENV["EOMSTAR"] = "#{scrbody}.F80"
	287	+ ENV["EOMVEC1"] = "#{scrbody}.F81"
	288	+ ENV["EOMVEC2"] = "#{scrbody}.F82"
	289	+ ENV["EOMHC1"] = "#{scrbody}.F83"
	290	+ ENV["EOMHC2"] = "#{scrbody}.F84"
	291	+ ENV["EOMHHHH"] = "#{scrbody}.F85"
	292	+ ENV["EOMPPPP"] = "#{scrbody}.F86"
	293	+ ENV["EOMRAMP"] = "#{scrbody}.F87"
	294	+ ENV["EOMRTMP"] = "#{scrbody}.F88"
	295	+ ENV["EOMDG12"] = "#{scrbody}.F89"
	296	+ ENV["MMPP"] = "#{scrbody}.F90"
	297	+ ENV["MMHPP"] = "#{scrbody}.F91"
	298	+ ENV["MMCIVEC"] = "#{scrbody}.F92"
	299	+ ENV["MMCIVC1"] = "#{scrbody}.F93"
	300	+ ENV["MMCIITR"] = "#{scrbody}.F94"
	301	+ ENV["MMNEXM"] = "#{scrbody}.F95"
	302	+ ENV["MMNEXE"] = "#{scrbody}.F96"
	303	+ ENV["MMNREXM"] = "#{scrbody}.F97"
	304	+ ENV["MMNREXE"] = "#{scrbody}.F98 "
300	305	#
301	306	# next are for TDHFX code, not used by current GAMESS
302	307	#
303		- ENV["OLI201"] = "#{scrprefix}.F201"
304		- ENV["OLI202"] = "#{scrprefix}.F202"
305		- ENV["OLI203"] = "#{scrprefix}.F203"
306		- ENV["OLI204"] = "#{scrprefix}.F204"
307		- ENV["OLI205"] = "#{scrprefix}.F205"
308		- ENV["OLI206"] = "#{scrprefix}.F206"
309		- ENV["OLI207"] = "#{scrprefix}.F207"
310		- ENV["OLI208"] = "#{scrprefix}.F208"
311		- ENV["OLI209"] = "#{scrprefix}.F209"
312		- ENV["OLI210"] = "#{scrprefix}.F210"
313		- ENV["OLI211"] = "#{scrprefix}.F211"
314		- ENV["OLI212"] = "#{scrprefix}.F212"
315		- ENV["OLI213"] = "#{scrprefix}.F213"
316		- ENV["OLI214"] = "#{scrprefix}.F214"
317		- ENV["OLI215"] = "#{scrprefix}.F215"
318		- ENV["OLI216"] = "#{scrprefix}.F216"
319		- ENV["OLI217"] = "#{scrprefix}.F217"
320		- ENV["OLI218"] = "#{scrprefix}.F218"
321		- ENV["OLI219"] = "#{scrprefix}.F219"
322		- ENV["OLI220"] = "#{scrprefix}.F220"
323		- ENV["OLI221"] = "#{scrprefix}.F221"
324		- ENV["OLI222"] = "#{scrprefix}.F222"
325		- ENV["OLI223"] = "#{scrprefix}.F223"
326		- ENV["OLI224"] = "#{scrprefix}.F224"
327		- ENV["OLI225"] = "#{scrprefix}.F225"
328		- ENV["OLI226"] = "#{scrprefix}.F226"
329		- ENV["OLI227"] = "#{scrprefix}.F227"
330		- ENV["OLI228"] = "#{scrprefix}.F228"
331		- ENV["OLI229"] = "#{scrprefix}.F229"
332		- ENV["OLI230"] = "#{scrprefix}.F230"
333		- ENV["OLI231"] = "#{scrprefix}.F231"
334		- ENV["OLI232"] = "#{scrprefix}.F232"
335		- ENV["OLI233"] = "#{scrprefix}.F233"
336		- ENV["OLI234"] = "#{scrprefix}.F234"
337		- ENV["OLI235"] = "#{scrprefix}.F235"
338		- ENV["OLI236"] = "#{scrprefix}.F236"
339		- ENV["OLI237"] = "#{scrprefix}.F237"
340		- ENV["OLI238"] = "#{scrprefix}.F238"
341		- ENV["OLI239"] = "#{scrprefix}.F239"
	308	+ ENV["OLI201"] = "#{scrbody}.F201"
	309	+ ENV["OLI202"] = "#{scrbody}.F202"
	310	+ ENV["OLI203"] = "#{scrbody}.F203"
	311	+ ENV["OLI204"] = "#{scrbody}.F204"
	312	+ ENV["OLI205"] = "#{scrbody}.F205"
	313	+ ENV["OLI206"] = "#{scrbody}.F206"
	314	+ ENV["OLI207"] = "#{scrbody}.F207"
	315	+ ENV["OLI208"] = "#{scrbody}.F208"
	316	+ ENV["OLI209"] = "#{scrbody}.F209"
	317	+ ENV["OLI210"] = "#{scrbody}.F210"
	318	+ ENV["OLI211"] = "#{scrbody}.F211"
	319	+ ENV["OLI212"] = "#{scrbody}.F212"
	320	+ ENV["OLI213"] = "#{scrbody}.F213"
	321	+ ENV["OLI214"] = "#{scrbody}.F214"
	322	+ ENV["OLI215"] = "#{scrbody}.F215"
	323	+ ENV["OLI216"] = "#{scrbody}.F216"
	324	+ ENV["OLI217"] = "#{scrbody}.F217"
	325	+ ENV["OLI218"] = "#{scrbody}.F218"
	326	+ ENV["OLI219"] = "#{scrbody}.F219"
	327	+ ENV["OLI220"] = "#{scrbody}.F220"
	328	+ ENV["OLI221"] = "#{scrbody}.F221"
	329	+ ENV["OLI222"] = "#{scrbody}.F222"
	330	+ ENV["OLI223"] = "#{scrbody}.F223"
	331	+ ENV["OLI224"] = "#{scrbody}.F224"
	332	+ ENV["OLI225"] = "#{scrbody}.F225"
	333	+ ENV["OLI226"] = "#{scrbody}.F226"
	334	+ ENV["OLI227"] = "#{scrbody}.F227"
	335	+ ENV["OLI228"] = "#{scrbody}.F228"
	336	+ ENV["OLI229"] = "#{scrbody}.F229"
	337	+ ENV["OLI230"] = "#{scrbody}.F230"
	338	+ ENV["OLI231"] = "#{scrbody}.F231"
	339	+ ENV["OLI232"] = "#{scrbody}.F232"
	340	+ ENV["OLI233"] = "#{scrbody}.F233"
	341	+ ENV["OLI234"] = "#{scrbody}.F234"
	342	+ ENV["OLI235"] = "#{scrbody}.F235"
	343	+ ENV["OLI236"] = "#{scrbody}.F236"
	344	+ ENV["OLI237"] = "#{scrbody}.F237"
	345	+ ENV["OLI238"] = "#{scrbody}.F238"
	346	+ ENV["OLI239"] = "#{scrbody}.F239"
342	347
343	348	if $platform == "win"
344	349	if ncpus < 2

		@@ -355,7 +360,7 @@ class Molecule
355	360	# File containing arguments to mpiexec
356	361	procfil = "#{scrprefix}.processes.mpd"
357	362	fp = File.open(procfil, "w")
358		- fp.print "-env ENVFIL #{envfil} -n #{ncpus} #{gmsdir}#{sep}gamess.#{gmsvers}.exe\n"
	363	+ fp.print "-env ENVFIL #{envfil} -wdir #{scrdir} -n #{ncpus} #{gmsdir}#{sep}gamess.#{gmsvers}.exe\n"
359	364	fp.close
360	365	end
361	366

--- a/Scripts/startup.rb

+++ b/Scripts/startup.rb

		@@ -23,14 +23,15 @@ $startup_dir = Dir.pwd
23	23	case RUBY_PLATFORM
24	24	when /mswin\|mingw\|cygwin\|bccwin/
25	25	$platform = "win"
26		-# $KCODE="SJIS"
	26	+ Encoding.default_external = "shift_jis"
27	27	$home_directory = ENV['USERPROFILE'].gsub(/\\/, "/")
28	28	when /darwin/
29	29	$platform = "mac"
30		-# $KCODE="UTF8"
	30	+ Encoding.default_external = "utf-8"
31	31	$home_directory = ENV['HOME']
32	32	else
33	33	$platform = "other"
	34	+ Encoding.default_external = "locale"
34	35	$home_directory = ENV['HOME']
35	36	end
36	37

--- a/Scripts/view.rb

+++ b/Scripts/view.rb

		@@ -123,24 +123,24 @@ end
123	123
124	124	register_menu("View\t-", nil)
125	125	register_menu("View\t^Show Unit Cell", :cmd_show_unit_cell,
126		- lambda { \|m\| [m != nil, m.show_unitcell] } )
	126	+ lambda { \|m\| [m != nil, m && m.show_unitcell] } )
127	127	register_menu("View\t^Show Hydrogen Atoms", :cmd_show_hydrogens,
128		- lambda { \|m\| [m != nil, m.show_hydrogens] } )
	128	+ lambda { \|m\| [m != nil, m && m.show_hydrogens] } )
129	129	register_menu("View\t^Show Dummy Atoms", :cmd_show_dummy_atoms,
130		- lambda { \|m\| [m != nil, m.show_dummy_atoms] } )
	130	+ lambda { \|m\| [m != nil, m && m.show_dummy_atoms] } )
131	131	register_menu("View\t^Show Expanded Atoms", :cmd_show_expanded,
132		- lambda { \|m\| [m != nil, m.show_expanded] } )
	132	+ lambda { \|m\| [m != nil, m && m.show_expanded] } )
133	133	register_menu("View\t^Show Ellipsoids", :cmd_show_ellipsoids,
134		- lambda { \|m\| [m != nil, m.show_ellipsoids] } )
	134	+ lambda { \|m\| [m != nil, m && m.show_ellipsoids] } )
135	135	register_menu("View\t^Show Rotation Center", :cmd_show_rotation_center,
136		- lambda { \|m\| [m != nil, m.show_rotation_center] } )
	136	+ lambda { \|m\| [m != nil, m && m.show_rotation_center] } )
137	137	register_menu("View\t-", nil)
138	138	register_menu("View\t^Show Graphite...", :cmd_show_graphite,
139		- lambda { \|m\| [m != nil, m.show_graphite?] } )
	139	+ lambda { \|m\| [m != nil, m && m.show_graphite?] } )
140	140	register_menu("View\t-", nil)
141	141	register_menu("View\tAppearance\t^Line", :cmd_line_mode,
142		- lambda { \|m\| [m != nil, m.line_mode] } )
	142	+ lambda { \|m\| [m != nil, m && m.line_mode] } )
143	143	register_menu("View\tAppearance\t^Ball and Stick", :cmd_ball_and_stick_mode,
144		- lambda { \|m\| [m != nil, !m.line_mode && m.atom_radius < 0.5] } )
	144	+ lambda { \|m\| [m != nil, m && !m.line_mode && m.atom_radius < 0.5] } )
145	145	register_menu("View\tAppearance\t^Space Filling", :cmd_space_filling_mode,
146		- lambda { \|m\| [m != nil, !m.line_mode && m.atom_radius >= 0.5] } )
	146	+ lambda { \|m\| [m != nil, m && !m.line_mode && m.atom_radius >= 0.5] } )

--- a/how_to_build

+++ b/how_to_build

		@@ -44,6 +44,7 @@ Get ruby-2.0.0-p353.tar.gz, unpack it, and move the resulting directory ruby-2.0
44	44	$ cd $MOLBY/../ruby-2.0.0-p353
45	45	$ CFLAGS='-isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -O2' ./configure --prefix=$PWD/osx-build --with-arch=i386,ppc --disable-shared --with-ext=date --disable-install-rdoc
46	46	$ make && make install
	47	+$ cd enc; ar -r libenc.a *.o; cp libenc.a ../osx-build/lib # We need shift_jis.o etc. for encoding support
47	48
48	49	The osx-build directory contains lib (which contains libruby-static.a) and include (which contains include files). (There are also bin and share directories, but these are not used for building Molby.)
49	50	$ make clean # Remove configure files and intermediates; the osx-build directory remains intact

		@@ -118,6 +119,7 @@ If you use gcc 4.6 or later, comment out the following line in cygwin/GNUmakefil
118	119
119	120	$ ./configure --prefix=$PWD/msw-build --disable-shared --with-ext=date --disable-install-rdoc --with-static-linked-ext
120	121	$ make && make install
	122	+$ cp enc/libenc.a msw-build/lib # We need this for encoding support
121	123
122	124	The msw-build directory contains lib (which contains libmsvcrt-ruby200-static.a and libmsvcrt-rubuy200.a) and include (which contains include files). (There are also bin and share directories, but these are not used for building Molby.)
123	125	$ make clean # Remove configure files and intermediates; the msw-build directory remains intact

--- a/wxSources/ConsoleFrame.cpp

+++ b/wxSources/ConsoleFrame.cpp

		@@ -364,10 +364,14 @@ ConsoleFrame::OnEnterPressed()
364	364	Molby_showError(status);
365	365	} else {
366	366	textCtrl->AppendText(wxT("-->"));
367		- Molby_showRubyValue(val, &valueString);
368		- AssignArray(&valueHistory, &nValueHistory, sizeof(char *), nValueHistory, &valueString);
369		- if (nValueHistory >= MAX_HISTORY_LINES)
370		- DeleteArray(&valueHistory, &nValueHistory, sizeof(char *), 0, 1, NULL);
	367	+ status = Molby_showRubyValue(val, &valueString);
	368	+ if (status != 0) {
	369	+ Molby_showError(status);
	370	+ } else {
	371	+ AssignArray(&valueHistory, &nValueHistory, sizeof(char *), nValueHistory, &valueString);
	372	+ if (nValueHistory >= MAX_HISTORY_LINES)
	373	+ DeleteArray(&valueHistory, &nValueHistory, sizeof(char *), 0, 1, NULL);
	374	+ }
371	375	}
372	376	MyAppCallback_setConsoleColor(0);
373	377	textCtrl->AppendText(wxT("\n"));

--- a/wxSources/MyApp.cpp

+++ b/wxSources/MyApp.cpp

		@@ -43,6 +43,7 @@
43	43	#include "wx/process.h"
44	44	#include "wx/utils.h"
45	45	#include "wx/sound.h"
	46	+#include "wx/time.h"
46	47
47	48	#include "MyApp.h"
48	49	#include "MyDocument.h"

		@@ -1238,6 +1239,7 @@ MyApp::CallSubProcess(const char cmdline, const char procname, int (*callback)
1238	1239	char buf[256];
1239	1240	size_t len, len_total;
1240	1241	wxString cmdstr(cmdline, WX_DEFAULT_CONV);
	1242	+ wxLongLong startTime;
1241	1243
1242	1244	if (m_process != NULL)
1243	1245	return -1; // Another process is already running (CallSubProcess() allows only one subprocess)

		@@ -1251,6 +1253,7 @@ MyApp::CallSubProcess(const char cmdline, const char procname, int (*callback)
1251	1253	ShowProgressPanel(buf);
1252	1254	progress_panel = true;
1253	1255	}
	1256	+ startTime = wxGetUTCTimeMillis();
1254	1257
1255	1258	// Create log file in the document home directory
1256	1259	#if LOG_SUBPROCESS

		@@ -1342,8 +1345,9 @@ MyApp::CallSubProcess(const char cmdline, const char procname, int (*callback)
1342	1345	}
1343	1346	}
1344	1347	}
1345		- if (++count == 100) {
1346		- if (progress_panel == false) {
	1348	+ if (progress_panel == false) {
	1349	+ ::wxSafeYield(NULL); // This seems necessary to get OnEndProcess called
	1350	+ if (++count == 40) {
1347	1351	ShowProgressPanel("Running subprocess...");
1348	1352	progress_panel = true;
1349	1353	}

		@@ -1431,7 +1435,7 @@ MyApp::CallSubProcess(const char cmdline, const char procname, int (*callback)
1431	1435	nn = 0;
1432	1436	}
1433	1437	#endif
1434		- ::wxMilliSleep(10);
	1438	+ ::wxMilliSleep(25);
1435	1439	if (wxGetApp().IsInterrupted() \|\| (callback != NULL && callback != DUMMY_CALLBACK && (callback_result = (*callback)(callback_data)) != 0)) {
1436	1440	/* User interrupt */
1437	1441	int kflag = wxKILL_CHILDREN;

		@@ -1894,7 +1898,7 @@ MyAppCallback_executeScriptFromFile(const char cpath, int status)
1894	1898	}
1895	1899
1896	1900	/* Check the encoding specification, and if present convert it to default encoding */
1897		- {
	1901	+ if (0) {
1898	1902	char lp = script, eolp;
1899	1903	int n = 0;
1900	1904	while (n < 2) { /* Check the first two lines */

--- a/xcode-build/Molby.xcodeproj/project.pbxproj

+++ b/xcode-build/Molby.xcodeproj/project.pbxproj

		@@ -667,6 +667,7 @@
667	667	"-liconv",
668	668	"-lfftw3",
669	669	"-lruby-static",
	670	+ "-lenc",
670	671	);
671	672	PRODUCT_NAME = Molby;
672	673	SDKROOT = macosx10.5;

		@@ -722,6 +723,7 @@
722	723	"-liconv",
723	724	"-lfftw3",
724	725	"-lruby-static",
	726	+ "-lenc",
725	727	);
726	728	PRODUCT_NAME = Molby;
727	729	SDKROOT = macosx10.5;

		@@ -786,6 +788,7 @@
786	788	OTHER_LDFLAGS = (
787	789	"-lfftw3",
788	790	"-lruby-static",
	791	+ "-lenc",
789	792	);
790	793	PREBINDING = NO;
791	794	PRODUCT_NAME = Molby_command;

		@@ -816,6 +819,7 @@
816	819	OTHER_LDFLAGS = (
817	820	"-lfftw3",
818	821	"-lruby-static",
	822	+ "-lenc",
819	823	);
820	824	PREBINDING = NO;
821	825	PRODUCT_NAME = Molby_command;

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