Recent changes to debug-practice

debug-practice modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sat, 14 Sep 2024 03:38:44 -0000

--- v7
+++ v8
@@ -11,7 +11,7 @@
 diff soln_old soln_new
 ~~~~

-tests the differences of all the output files at once, and no difference is supposed to be seen for the ermod outputs if the modification is correct.
+tests the differences of all the output files at once, and no difference is supposed to be seen for the erdst outputs if the modification is correct.

 For the refs run, in contrast, a similar procedure does not work at the default setting.
 This is because the seed of the random number used for insertion is generated randomly in the default setting.
@@ -26,7 +26,7 @@
 ~~~~

 in the &ene_param section.
-With this setting, when the same parameters_er file as well as the same ones of the other files are fed to the ermod programs before and after the modification, the sequence of the random numbers is the same and the outputs are supposed to be the same.
+With this setting, when the same parameters_er file as well as the same ones of the other files are fed to the erdst programs before and after the modification, the sequence of the random numbers is the same and the outputs are supposed to be the same.

 ~~~~sh
 diff refs_old refs_new

debug-practice modified by Shun Sakuraba

Shun Sakuraba — Fri, 12 Apr 2024 01:47:24 -0000

--- v6
+++ v7
@@ -7,8 +7,7 @@
 This practice works readily for the soln system.
 When the directories of soln_old and soln_new have the results from the programs before and after the modification, respectively,

-~~~~
-::::text
+~~~~text
 diff soln_old soln_new
 ~~~~

@@ -23,14 +22,13 @@
 It is enough to open the parameters_er file and add a line of

 ~~~~
-iseed = (any non-zero number within 9 digits, e.g., 123456789),
+iseed = (any non-zero number within 18 digits, e.g., 123456789),
 ~~~~

 in the &ene_param section.
 With this setting, when the same parameters_er file as well as the same ones of the other files are fed to the ermod programs before and after the modification, the sequence of the random numbers is the same and the outputs are supposed to be the same.

-~~~~
-::::text
+~~~~sh
 diff refs_old refs_new
 ~~~~

debug-practice modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sat, 25 Jul 2015 15:20:56 -0000

--- v5
+++ v6
@@ -1,8 +1,8 @@
 Debugging practice for the reference-solvent calculation
 ====

-When some modification is made for the program, it is a common practice that a same input is fed to the programs before and after the modification.
-If the modification of the program is not meant to change the results from that input, this practice is useful to detect a possible bug.
+When some modification is made for the program, it is a common practice that same inputs are fed to the programs before and after the modification.
+If the modification of the program is not meant to change the results from those inputs, this practice is useful to detect a possible bug.

 This practice works readily for the soln system.
 When the directories of soln_old and soln_new have the results from the programs before and after the modification, respectively,
@@ -16,10 +16,10 @@

 For the refs run, in contrast, a similar procedure does not work at the default setting.
 This is because the seed of the random number used for insertion is generated randomly in the default setting.
-Even when everything else is common, two refs runs provide different results if the random number seed is different.
-This property is not convenient for debugging.
+Even when everything else is common, two refs runs provide different results if the random-number seed is different.
+It is not convenient for debugging.

-For the debugging purpose, a convenient scheme is to fix the random number seed.
+For the debugging purpose, a convenient scheme is to fix the random-number seed.
 It is enough to open the parameters_er file and add a line of

 ~~~~

debug-practice modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sat, 25 Jul 2015 15:12:24 -0000

--- v4
+++ v5
@@ -1,4 +1,4 @@
-Debugging practice for reference-solvent simulation
+Debugging practice for the reference-solvent calculation
 ====

 When some modification is made for the program, it is a common practice that a same input is fed to the programs before and after the modification.

debug-practice modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sat, 25 Jul 2015 15:11:18 -0000

--- v3
+++ v4
@@ -1,18 +1,18 @@
-Debugging practice for reference-solvent calculation
+Debugging practice for reference-solvent simulation
 ====

 When some modification is made for the program, it is a common practice that a same input is fed to the programs before and after the modification.
 If the modification of the program is not meant to change the results from that input, this practice is useful to detect a possible bug.

 This practice works readily for the soln system.
-When the directories of soln_old and soln_new have the results from the programs before and after the modification,
+When the directories of soln_old and soln_new have the results from the programs before and after the modification, respectively,

 ~~~~
 ::::text
 diff soln_old soln_new
 ~~~~

-tests the differences of all the output files at once, and no difference is supposed to be seen for the ermod outputs if the modification is fine.
+tests the differences of all the output files at once, and no difference is supposed to be seen for the ermod outputs if the modification is correct.

 For the refs run, in contrast, a similar procedure does not work at the default setting.
 This is because the seed of the random number used for insertion is generated randomly in the default setting.
@@ -34,4 +34,4 @@
 diff refs_old refs_new
 ~~~~

-is then convenient to test the differences all at once, where refs_old and refs_new are the directories for the results from the ermod runs before and after the modification.
+is then convenient to test the differences all at once, where refs_old and refs_new are the directories for the results from the ermod runs before and after the modification, respectively.

WikiPage refs-iseed modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 04 May 2012 14:06:07 -0000

--- v2 
+++ v3 
@@ -12,10 +12,13 @@
 diff soln_old soln_new
 ~~~~
 
-tests the differences of all the output files at once.
-
+tests the differences of all the output files at once, and no difference is supposed to be seen for the ermod outputs if the modification is fine.
+
 For the refs run, in contrast, a similar procedure does not work at the default setting.
-This is because the seed of the random number used for insertions is generated randomly in the default setting.
+This is because the seed of the random number used for insertion is generated randomly in the default setting.
+Even when everything else is common, two refs runs provide different results if the random number seed is different.
+This property is not convenient for debugging.
+
 For the debugging purpose, a convenient scheme is to fix the random number seed.
 It is enough to open the parameters_er file and add a line of

WikiPage refs-iseed modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 04 May 2012 13:55:24 -0000

--- v1 
+++ v2 
@@ -20,7 +20,7 @@
 It is enough to open the parameters_er file and add a line of
 
 ~~~~
-iseed = (any number within 9 digits, e.g., 123456789),
+iseed = (any non-zero number within 9 digits, e.g., 123456789),
 ~~~~
 
 in the &ene_param section.

WikiPage refs-iseed modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 04 May 2012 13:29:31 -0000

Debugging practice for reference-solvent calculation ==== When some modification is made for the program, it is a common practice that a same input is fed to the programs before and after the modification. If the modification of the program is not meant to change the results from that input, this practice is useful to detect a possible bug. This practice works readily for the soln system. When the directories of soln_old and soln_new have the results from the programs before and after the modification, ~~~~ ::::text diff soln_old soln_new ~~~~ tests the differences of all the output files at once. For the refs run, in contrast, a similar procedure does not work at the default setting. This is because the seed of the random number used for insertions is generated randomly in the default setting. For the debugging purpose, a convenient scheme is to fix the random number seed. It is enough to open the parameters_er file and add a line of ~~~~ iseed = (any number within 9 digits, e.g., 123456789), ~~~~ in the &ene_param section. With this setting, when the same parameters_er file as well as the same ones of the other files are fed to the ermod programs before and after the modification, the sequence of the random numbers is the same and the outputs are supposed to be the same. ~~~~ ::::text diff refs_old refs_new ~~~~ is then convenient to test the differences all at once, where refs_old and refs_new are the directories for the results from the ermod runs before and after the modification.