Recent changes to parameters-slvfe

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sat, 06 Feb 2021 05:57:34 -0000

--- v44
+++ v45
@@ -26,7 +26,7 @@
 Description of each parameter
 ----

-Before the description of the parameters, group and inft variables in the slvfe.F90 program are explained. These are described in the Appendix of Matubayasi's "part II" paper (J. Chem. Phys. 117, 3605 (2002)) and correspond to the procedures for Eqs. (A5) and (A6), respectively. The variable group coarsens the energy meshes, and inft is to validate (or invalidate) the choice of the maximum energy mesh.
+Before the description of the parameters, group and inft variables in the slvfe.F90 program are explained. These are described in the Appendix of J. Chem. Phys. 117, 3605 (2002) and correspond to the procedures for Eqs. (A5) and (A6), respectively. The variable group coarsens the energy meshes, andinft is to validate (or invalidate) the choice of the maximum energy mesh.

 ##### clcond

@@ -44,17 +44,17 @@
 ##### numsln

 Number of engsln files.
-Taken from the number in the soln directory as the default, and effective only when clcond = 'merge'
+Taken from the number in the soln directory as the default, and effective only when clcond = 'merge'

 ##### numref

 Number of engref and corref files.
-Taken from the number in the refs directory as the default, and effective only when clcond = 'merge'
+Taken from the number in the refs directory as the default, and effective only when clcond = 'merge'

 ##### numdiv

 Number of division of the blocks in the soln run.
-Set to be equal to numsln as the default, and effective only when clcond = 'merge'
+Set to be equal to numsln as the default, and effective only when clcond = 'merge'

 ##### ljlrc

@@ -66,15 +66,15 @@

 ##### uvread

-If ‘yes’, reading the average sum of solute-solvent interaction energy from a file. The default is ‘yes’, and the filename is soln/aveuv.tt when clcond is ‘merge’ (default) and the average sum vale needs to be input in the other clcond cases. If uvread = ‘not’, the average sum of solute-solvent interaction energy is constructed from engsln files. If ‘not’, the average sum will have some mesh error originating from the meshed distribution engsln. If ‘yes’, the average sum is free from the mesh error.
+If ‘yes’, reading the average sum of solute-solvent interaction energy from a file. The default is ‘yes’, and the filename is soln/aveuv.tt when clcond is ‘merge’ (default) and the average sum vale needs to be input in the other clcond cases. If uvread = ‘not’, the average sum of solute-solvent interaction energy is constructed from engsln files. If ‘not’, the average sum will have some mesh error originating from the meshed distribution engsln. If ‘yes’, the average sum is free from the mesh error.

 ##### slfslt

-Key for the self-energy correction to the solvation free energy and the average sum of solute-solvent interaction energy. If ‘yes’, the correction value is taken from refs/weight_refs. The default is ‘yes’ when the periodic boundary condition is employed in the parent MD, and is ‘not’ in the other cases.
+Key for the self-energy correction to the solvation free energy and the average sum of solute-solvent interaction energy. If ‘yes’, the correction value is taken from refs/weight_refs. The default is ‘yes’, and is to be changed into 'not' when the periodic boundary condition is not employed in the parent MD.

 ##### normalize

-If ‘yes’ (default), normalizing the engsln and engref files and enforcing consistency condition for corref file described in the Appendix C of part III paper.
+If ‘yes’ (default), normalizing the engsln and engref files and enforcing consistency condition for corref file described in the Appendix C of J. Chem. Phys. 119, 9686-9702 (2003).

 ##### showdst

@@ -99,7 +99,7 @@
 ##### write_mesherror

 If ‘not’, the mesh error is not shown.
-If ‘yes’, the mesh error is shown as a warning at the end of the slvfe output.
+If ‘yes’, the mesh error is shown at the end of the slvfe output.
 Otherwise (default), the mesh error is not shown when it is smaller than mesherr defined below.
 When the mesh error is larger than mesherr at the default setting of write_mesherror,
 it is provided as an output in the following, two cases.
@@ -119,10 +119,12 @@
 or 2) when the mesh error is smaller than the 95% error and it is larger than mesherr defined next.
 Case 2) provides the mesh error as an output only when mesherr is set to be positive (not an output when mesherr is equal to or less than 0).

+When the ERmod version is 0.3.5 or earlier, the mesh error is shown as a warning when it is larger than mesherr provided next.
+
 ##### mesherr

-Threshold value to give a warning message of mesh error in case 2) above. The default setting is 0.
-When the ERmod version is 0.3.5 or earlier, the mesh error is shown as a warning when it is larger than mesherr; the default = 0.1 kcal/mol.
+Threshold value to give a warning message of mesh error described above. The default setting is 0.1 kcal/mol.
+Only at ver 0.3.6, the default is 0.

 ##### infchk

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Tue, 13 Oct 2020 03:57:53 -0000

--- v43
+++ v44
@@ -58,7 +58,7 @@

 ##### ljlrc

-Key for the long-range correction of the Lennard-Jones interaction between the solute and solvent. The default is 'not', and the long-range correction is performed when ljlrc is set to 'yes'. See  [Lennard-Jones long-range correction](LongRangeCorrectionLJ) for the usage at ljlrc = 'yes' and a **caution**. Effective as of ver 0.3.5
+Key for the long-range correction of the Lennard-Jones interaction between the solute and solvent. The default is 'not', and the long-range correction is performed when ljlrc is set to 'yes'. See [Lennard-Jones long-range correction](LongRangeCorrectionLJ) for the usage at ljlrc = 'yes' and a **caution**. Effective as of ver 0.3.5

 ##### avevolume

@@ -173,7 +173,7 @@
 ##### cumuint
 ##### cumuintfl

-In an slvfe calculation, the solvation free energy is calculated through integration over the energy coordinate ¥epsilon from -¥infty to ¥infty. When cumuint = 'yes', slvfe outputs the running integral from -¥infty to ¥epsilon as a function of ¥epsilon to the cumuintfl file; cumuintfl is the name of the output file storing the running integral when the option cumuint is 'yes'. The self-energy correction is not applied to the running-integral values. Thus, although the last line in the cumuintfl file corresponds to the integral from -¥infty to ¥infty, it deviates from the total solvation free energy given as an slvfe output since the the self energy is added to the total free energy and not to the running integrals in cumuintfl. In this sense, the values in cumuintfl reflects only the intermolecular effects. The default for cumuint is 'not', and the default for cumuintfl is 'cumsfe'. Effective as of ver 0.3.alpha5
+Key for providing the running integral as an output. The default is 'not' for cumuint, and cumuintfl is active only when cumuint = 'yes'.. See [Running integral over the energy coordinate, and the estimation of the excluded-volume contribution](RunningIntegral) for the usage at cumuint = 'yes''. Effective as of ver 0.3.7

 ##### extthres_soln
 ##### extthres_refs

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 May 2020 07:34:54 -0000

--- v42
+++ v43
@@ -109,14 +109,15 @@
 it is shown in the format of "Warning: mesh error is larger than the threshold value of mesherr"
 Case 1) precedes case 2), and in case 1), the mesh error is  larger than both the 95% error and mesherr.
 In case 2), the mesh error is  smaller than  the 95% error and  it is larger than mesherr.
+Case 2) provides the mesh error as an output only when mesherr is set to be positive (not an output when mesherr is equal to or less than 0).
 Effective as of ver 0.3.7.

 At ver 0.3.6, the key of write_mesherror works differently.
 If ‘yes’, the mesh error is shown at the end of the slvfe output.
 Otherwise (default), the mesh error is shown
 1) when it is larger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy
-or 2) when the mesh error is smaller than the 95% error and it is larger than mesherr defined next.
-Case 2) provides the mesh error as an output of slvfe only when mesherr is set to be positive (not an output when mesherr is equal to or less than 0).
+or 2) when the mesh error is smaller than the 95% error and it is larger than mesherr defined next.
+Case 2) provides the mesh error as an output only when mesherr is set to be positive (not an output when mesherr is equal to or less than 0).

 ##### mesherr

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 May 2020 07:25:38 -0000

--- v41
+++ v42
@@ -32,9 +32,9 @@

 Type of handling the set of files. Three types are prepared: ‘basic’, ‘range’, and ‘merge’ (default)

-* *basic:* takes one set of engsln.XX, engref.XX, and corref.XX and further takes group and inft parameters
-* *range:* extended option with automatic examination of the mesh error. The group and inft variables are changed internally in the program. The integer parameter numprm determines how many variations are conducted, and the variable settings (group and inft) are described within the subroutine defcond in the program slvfe.F90. To change variable settings, open the source and modify numprm and the subroutine defcond.
-merge: (default) most extended option with automatic examination of the mesh error and treatment of multiple files. This option examines both the mesh error and statistical error
+* basic: takes one set of engsln.XX, engref.XX, and corref.XX and further takes group and inft parameters
+* range: extended option with automatic examination of the mesh error. The group and inft variables are changed internally in the program. The integer parameter numprm determines how many variations are conducted, and the variable settings (group and inft) are described within the subroutine defcond in the program slvfe.F90. To change variable settings, open the source and modify numprm and the subroutine defcond.
+* merge: (default) most extended option with automatic examination of the mesh error and treatment of multiple files. This option examines both the mesh error and statistical error

 ##### numprm

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 May 2020 07:23:33 -0000

--- v40
+++ v41
@@ -34,7 +34,7 @@

 * *basic:* takes one set of engsln.XX, engref.XX, and corref.XX and further takes group and inft parameters
 * *range:* extended option with automatic examination of the mesh error. The group and inft variables are changed internally in the program. The integer parameter numprm determines how many variations are conducted, and the variable settings (group and inft) are described within the subroutine defcond in the program slvfe.F90. To change variable settings, open the source and modify numprm and the subroutine defcond.
-* *merge:* (default) most extended option with automatic examination of the mesh error and treatment of multiple files. This option examines both the mesh error and statistical error
+merge: (default) most extended option with automatic examination of the mesh error and treatment of multiple files. This option examines both the mesh error and statistical error

 ##### numprm

@@ -103,7 +103,7 @@
 Otherwise (default), the mesh error is not shown when it is smaller than mesherr defined below.
 When the mesh error is larger than mesherr at the default setting of write_mesherror,
 it is provided as an output in the following, two cases.
-1) When the mesh error is arger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy,
+1) When the mesh error is larger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy,
 it is shown in the format of "Warning: mesh error is larger than 95% error"
 2) When the mesh error is smaller than the 95% error,
 it is shown in the format of "Warning: mesh error is larger than the threshold value of mesherr"

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 May 2020 07:21:21 -0000

--- v39
+++ v40
@@ -102,7 +102,7 @@
 If ‘yes’, the mesh error is shown as a warning at the end of the slvfe output.
 Otherwise (default), the mesh error is not shown when it is smaller than mesherr defined below.
 When the mesh error is larger than mesherr at the default setting of write_mesherror,
-it is shown in the following, two cases.
+it is provided as an output in the following, two cases.
 1) When the mesh error is arger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy,
 it is shown in the format of "Warning: mesh error is larger than 95% error"
 2) When the mesh error is smaller than the 95% error,

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 May 2020 07:20:31 -0000

--- v38
+++ v39
@@ -104,9 +104,9 @@
 When the mesh error is larger than mesherr at the default setting of write_mesherror,
 it is shown in the following, two cases.
 1) When the mesh error is arger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy,
-it is shown as "Warning: mesh error is larger than 95% error"
+it is shown in the format of "Warning: mesh error is larger than 95% error"
 2) When the mesh error is smaller than the 95% error,
-it is shown as "Warning: mesh error is larger than the threshold value of mesherr"
+it is shown in the format of "Warning: mesh error is larger than the threshold value of mesherr"
 Case 1) precedes case 2), and in case 1), the mesh error is  larger than both the 95% error and mesherr.
 In case 2), the mesh error is  smaller than  the 95% error and  it is larger than mesherr.
 Effective as of ver 0.3.7.

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 May 2020 07:19:29 -0000

--- v37
+++ v38
@@ -99,11 +99,14 @@
 ##### write_mesherror

 If ‘not’, the mesh error is not shown.
-If ‘yes’, the mesh error is shown at the end of the slvfe output.
+If ‘yes’, the mesh error is shown as a warning at the end of the slvfe output.
 Otherwise (default), the mesh error is not shown when it is smaller than mesherr defined below.
 When the mesh error is larger than mesherr at the default setting of write_mesherror,
-it is shown against 1) the 95% error given in the last line for cumulative average & 95% error for solvation free energy
-or 2) the mesherr value.
+it is shown in the following, two cases.
+1) When the mesh error is arger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy,
+it is shown as "Warning: mesh error is larger than 95% error"
+2) When the mesh error is smaller than the 95% error,
+it is shown as "Warning: mesh error is larger than the threshold value of mesherr"
 Case 1) precedes case 2), and in case 1), the mesh error is  larger than both the 95% error and mesherr.
 In case 2), the mesh error is  smaller than  the 95% error and  it is larger than mesherr.
 Effective as of ver 0.3.7.

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 May 2020 07:06:56 -0000

--- v36
+++ v37
@@ -98,12 +98,22 @@

 ##### write_mesherror

-If ‘yes’, the mesh error is shown at the end of the ouput.
-If ‘not’ (default), the mesh error is shown
-1) when it is larger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy
-or 2) when the mesh error is smaller than the 95% error and it is larger than mesherr defined next.
-Case 2) provides the mesh error as an output of slvfe only when mesherr is set to be positive (not an output when mesherr = 0). 
-Effective as of ver 0.3.6.
+If ‘not’, the mesh error is not shown.
+If ‘yes’, the mesh error is shown at the end of the slvfe output.
+Otherwise (default), the mesh error is not shown when it is smaller than mesherr defined below.
+When the mesh error is larger than mesherr at the default setting of write_mesherror,
+it is shown against 1) the 95% error given in the last line for cumulative average & 95% error for solvation free energy
+or 2) the mesherr value.
+Case 1) precedes case 2), and in case 1), the mesh error is  larger than both the 95% error and mesherr.
+In case 2), the mesh error is  smaller than  the 95% error and  it is larger than mesherr.
+Effective as of ver 0.3.7.
+
+At ver 0.3.6, the key of write_mesherror works differently.
+If ‘yes’, the mesh error is shown at the end of the slvfe output.
+Otherwise (default), the mesh error is shown
+1) when it is larger than the 95% error given in the last line for cumulative average & 95% error for solvation free energy
+or 2) when the mesh error is smaller than the 95% error and it is larger than mesherr defined next.
+Case 2) provides the mesh error as an output of slvfe only when mesherr is set to be positive (not an output when mesherr is equal to or less than 0).

 ##### mesherr

parameters-slvfe modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Sun, 28 Apr 2019 13:36:32 -0000

--- v35
+++ v36
@@ -17,7 +17,6 @@
 slfslt = "yes",   ! "not" if the solute self energy is not read
 infchk = "yes",   ! Enable error analysis for the logarithmic-mesh part
 inptemp = 300e0,  ! Input Temperature in Kelvin
-mesherr = 0.1e0,  ! Maximum mesh error tolerance without producing a warning
 /
 ~~~~

@@ -33,29 +32,29 @@

 Type of handling the set of files. Three types are prepared: ‘basic’, ‘range’, and ‘merge’ (default)

-* *basic:* takes one set of engsln.XX, engref.XX, and corref.XX and further takes group and inft parameters
-* *range:* extended option with automatic examination of the mesh error. The group and inft variables are changed internally in the program. The integer parameter numprm determines how many variations are conducted, and the variable settings (group and inft) are described within the subroutine defcond in the program slvfe.F90. To change variable settings, open the source and modify numprm and the subroutine defcond.
+* *basic:* takes one set of engsln.XX, engref.XX, and corref.XX and further takes group and inft parameters
+* *range:* extended option with automatic examination of the mesh error. The group and inft variables are changed internally in the program. The integer parameter numprm determines how many variations are conducted, and the variable settings (group and inft) are described within the subroutine defcond in the program slvfe.F90. To change variable settings, open the source and modify numprm and the subroutine defcond.
 * *merge:* (default) most extended option with automatic examination of the mesh error and treatment of multiple files. This option examines both the mesh error and statistical error

 ##### numprm

-how many of group and inft sets are examined.
+How many of group and inft sets are examined.
 Active only when clcond = ‘range’ or ‘merge’

 ##### numsln

-number of engsln files.
-taken from the number in the soln directory as the default, and effective only when clcond = 'merge'
+Number of engsln files.
+Taken from the number in the soln directory as the default, and effective only when clcond = 'merge'

 ##### numref

-number of engref and corref files.
-taken from the number in the refs directory as the default, and effective only when clcond = 'merge'
+Number of engref and corref files.
+Taken from the number in the refs directory as the default, and effective only when clcond = 'merge'

 ##### numdiv

-number of division of the blocks in the soln run.
-set to be equal to numsln as the default, and effective only when clcond = 'merge'
+Number of division of the blocks in the soln run.
+Set to be equal to numsln as the default, and effective only when clcond = 'merge'

 ##### ljlrc

@@ -67,7 +66,7 @@

 ##### uvread

-if ‘yes’, reading the average sum of solute-solvent interaction energy from a file. The default is ‘yes’, and the filename is soln/aveuv.tt when clcond is ‘merge’ (default) and the average sum vale needs to be input in the other clcond cases. If uvread = ‘not’, the average sum of solute-solvent interaction energy is constructed from engsln files. If ‘not’, the average sum will have some mesh error originating from the meshed distribution engsln. If ‘yes’, the average sum is free from the mesh error.
+If ‘yes’, reading the average sum of solute-solvent interaction energy from a file. The default is ‘yes’, and the filename is soln/aveuv.tt when clcond is ‘merge’ (default) and the average sum vale needs to be input in the other clcond cases. If uvread = ‘not’, the average sum of solute-solvent interaction energy is constructed from engsln files. If ‘not’, the average sum will have some mesh error originating from the meshed distribution engsln. If ‘yes’, the average sum is free from the mesh error.

 ##### slfslt

@@ -83,19 +82,19 @@

 ##### inptemp

-temperature of the system, taken as the default from the parent MD setup
+Temperature of the system, taken as the default from the parent MD setup

 ##### pickgr

-identifying the group parameter to show the cumulative average in the last part of the slvfe output. The default value is 3
+Identifying the group parameter to show the cumulative average in the last part of the slvfe output. The default value is 3

 ##### msemin

-minimum group parameter to examine the mesh error. The default = 1.
+Minimum group parameter to examine the mesh error. The default = 1.

 ##### msemax

-maximum group parameter to examine the mesh error. The default = 5.
+Maximum group parameter to examine the mesh error. The default = 5.

 ##### write_mesherror

@@ -108,12 +107,12 @@

 ##### mesherr

-threshold value to give a warning message of mesh error in case 2) above. The default setting is 0.
+Threshold value to give a warning message of mesh error in case 2) above. The default setting is 0.
 When the ERmod version is 0.3.5 or earlier, the mesh error is shown as a warning when it is larger than mesherr; the default = 0.1 kcal/mol.

 ##### infchk

-key for specifying whether inft check is performed or not. The default is ‘not’
+Key for specifying whether inft check is performed or not. The default is ‘not’

 ##### meshread

@@ -174,7 +173,7 @@

 ##### pecore

-number of logarithmic meshes. The default value is 200.
+Number of logarithmic meshes. The default value is 200.
 As of ver 0.3.4, this parameter is internally determined within the slvfe.f90 program and is not used any more.

 ##### peread