Recent changes to output

output modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 29 Aug 2024 09:32:01 -0000

--- v31
+++ v32
@@ -136,7 +136,7 @@
 ----

 weight_soln is an output in a soln run and weight_refs is an output in a refs run.
-They give the statistical weight for each block of the MD trajectory; the number of blocks is specified by engdiv described in  [Parameter files for erdst](parameters-erdst).
+They give the statistical weight for each block of the MD trajectory; the number of blocks is specified by engdiv described in [Parameter files for erdst](parameters-erdst).
 When some average is to be taken over the blocks, the weights provided in weight_soln or weight_refs are assigned to the blocks.

 There are two formats of output depending on the value of wgtslf described in [Parameter files for erdst](parameters-erdst).

output modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 29 Aug 2024 09:30:38 -0000

--- v30
+++ v31
@@ -60,7 +60,7 @@

 aveuv.tt is an output only in a soln run.
 It provides the average sum of the solute-solvent interaction energy in each block of the MD trajectory in soln.
-As described in  [Parameter files for erdst](parameters-erdst), the MD trajectory in soln is divided in into a certain number of blocks specified by engdiv, and the average sum is given for each block.
+As described in [Parameter files for erdst](parameters-erdst), the MD trajectory in soln is divided in into a certain number of blocks specified by engdiv, and the average sum is given for each block.
 Typically, aveuv.tt reads like

 ~~~~

output modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 29 Aug 2024 09:28:49 -0000

--- v29
+++ v30
@@ -21,8 +21,8 @@
 The first and second columns in each line  correspond to the discretized, pair energy between solute and solvent.
 The first column refers to the beginning of the energy bin (smallest energy of the bin).
 The second column is the middle point of the energy bin. To be more precise, it is the middle of the end energies of the bin  when the energy is smaller than eccore described in  [Parameter files for erdst](parameters-erdst) and is the geometric mean of the end values  when the energy is larger than eccore. The end values are the values in the first columns in the same and next lines.
-The third column in each line identifies the solvent species. When its value is 2, for example, the line refers to the pair energy between the solute and the 2nd solvent species. Even when the solvent is not a mixed one and the number of solvent species is unity, the second column is present and is equal to 1.
-The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the first and second  columns and have the pair energy within the bin  specified by those columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
+The third column in each line identifies the solvent species. When its value is 2, for example, the line refers to the pair energy between the solute and the 2nd solvent species. Even when the solvent is not a mixed one and the number of solvent species is unity, the third column is present and is equal to 1.
+The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the third column and have the pair energy within the bin  specified by the first and second columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
 The fifth column is the density (i.e. the value in the fourth column / bin width).

output modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 29 Aug 2024 09:27:08 -0000

--- v28
+++ v29
@@ -19,7 +19,7 @@
 ~~~~

 The first and second columns in each line  correspond to the discretized, pair energy between solute and solvent.
-The first column in each line refers to the beginning of the energy bin (smallest energy of the bin).
+The first column refers to the beginning of the energy bin (smallest energy of the bin).
 The second column is the middle point of the energy bin. To be more precise, it is the middle of the end energies of the bin  when the energy is smaller than eccore described in  [Parameter files for erdst](parameters-erdst) and is the geometric mean of the end values  when the energy is larger than eccore. The end values are the values in the first columns in the same and next lines.
 The third column in each line identifies the solvent species. When its value is 2, for example, the line refers to the pair energy between the solute and the 2nd solvent species. Even when the solvent is not a mixed one and the number of solvent species is unity, the second column is present and is equal to 1.
 The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the first and second  columns and have the pair energy within the bin  specified by those columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.

output modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 29 Aug 2024 09:26:42 -0000

--- v27
+++ v28
@@ -20,7 +20,7 @@

 The first and second columns in each line  correspond to the discretized, pair energy between solute and solvent.
 The first column in each line refers to the beginning of the energy bin (smallest energy of the bin).
-The second column is the middle point of the energy mesh. To be more precise, it is the middle of the end energies of the bin  when the energy is smaller than eccore described in  [Parameter files for erdst](parameters-erdst) and is the geometric mean of the end values  when the energy is larger than eccore. The end values are the values in the first columns in the same and next lines.
+The second column is the middle point of the energy bin. To be more precise, it is the middle of the end energies of the bin  when the energy is smaller than eccore described in  [Parameter files for erdst](parameters-erdst) and is the geometric mean of the end values  when the energy is larger than eccore. The end values are the values in the first columns in the same and next lines.
 The third column in each line identifies the solvent species. When its value is 2, for example, the line refers to the pair energy between the solute and the 2nd solvent species. Even when the solvent is not a mixed one and the number of solvent species is unity, the second column is present and is equal to 1.
 The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the first and second  columns and have the pair energy within the bin  specified by those columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
 The fifth column is the density (i.e. the value in the fourth column / bin width).

output modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 29 Aug 2024 09:25:56 -0000

--- v26
+++ v27
@@ -20,9 +20,9 @@

 The first and second columns in each line  correspond to the discretized, pair energy between solute and solvent.
 The first column in each line refers to the beginning of the energy bin (smallest energy of the bin).
-The second column is the middle point of the energy mesh. To be more precise, it is the middle of the end energies of the mesh  when the energy is smaller than eccore described in  [Parameter files for erdst](parameters-erdst) and is the geometric mean of the end values  when the energy is larger than eccore. The end values are the values in the first columns in the same and next lines.
+The second column is the middle point of the energy mesh. To be more precise, it is the middle of the end energies of the bin  when the energy is smaller than eccore described in  [Parameter files for erdst](parameters-erdst) and is the geometric mean of the end values  when the energy is larger than eccore. The end values are the values in the first columns in the same and next lines.
 The third column in each line identifies the solvent species. When its value is 2, for example, the line refers to the pair energy between the solute and the 2nd solvent species. Even when the solvent is not a mixed one and the number of solvent species is unity, the second column is present and is equal to 1.
-The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the first and second  columns and have the pair energy within the mesh specified by those columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
+The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the first and second  columns and have the pair energy within the bin  specified by those columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
 The fifth column is the density (i.e. the value in the fourth column / bin width).

output modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 29 Aug 2024 09:24:51 -0000

--- v25
+++ v26
@@ -22,7 +22,7 @@
 The first column in each line refers to the beginning of the energy bin (smallest energy of the bin).
 The second column is the middle point of the energy mesh. To be more precise, it is the middle of the end energies of the mesh  when the energy is smaller than eccore described in  [Parameter files for erdst](parameters-erdst) and is the geometric mean of the end values  when the energy is larger than eccore. The end values are the values in the first columns in the same and next lines.
 The third column in each line identifies the solvent species. When its value is 2, for example, the line refers to the pair energy between the solute and the 2nd solvent species. Even when the solvent is not a mixed one and the number of solvent species is unity, the second column is present and is equal to 1.
-The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the first and second  columns and have the pair energy within the mesh specified i those columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
+The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the first and second  columns and have the pair energy within the mesh specified by those columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
 The fifth column is the density (i.e. the value in the fourth column / bin width).


@@ -39,8 +39,7 @@
 ~~~~

 The first, second, and third columns correspond to the second, third, and fourth columns in the above, respectively.
-It should be noted that the third column is the average histogram, not the density.
-To determine the pair-energy density, the value at the third column needs to be divided by the width of the corresponding mesh.
+It should be noted that the third column is the average histogram, not the density. To determine the pair-energy density, the value at the third column needs to be divided by the width of the corresponding mesh.

 engref.XX and corref.XX
 ----

output modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 29 Aug 2024 09:23:25 -0000

--- v24
+++ v25
@@ -1,4 +1,4 @@
-Outputs from ermod run
+Outputs from erdst run
 ====

 engsln.XX
@@ -6,7 +6,27 @@

 engsln.XX is an output only in a soln run.
 This output file is an input to the slvfe program to compute the solvation free energy.
-engsln.XX typically reads like **on Version 0.3 or below:**
+**As of version 1.0** ,engsln.XX typically reads like
+
+~~~~
+...
+  -4.370000      -4.345000        1    0.350465725129100E-01    0.700931450258191
+  -4.320000      -4.295000        1    0.380929927424355E-01    0.761859854848727
+  -4.270000      -4.245000        1    0.339955644632201E-01    0.679911289264393
+  -4.220000      -4.195000        1    0.429572985100842E-01    0.859145970201672
+  -4.170000      -4.145000        1    0.300335490894311E-01    0.600670981788636
+...
+~~~~
+
+The first and second columns in each line  correspond to the discretized, pair energy between solute and solvent.
+The first column in each line refers to the beginning of the energy bin (smallest energy of the bin).
+The second column is the middle point of the energy mesh. To be more precise, it is the middle of the end energies of the mesh  when the energy is smaller than eccore described in  [Parameter files for erdst](parameters-erdst) and is the geometric mean of the end values  when the energy is larger than eccore. The end values are the values in the first columns in the same and next lines.
+The third column in each line identifies the solvent species. When its value is 2, for example, the line refers to the pair energy between the solute and the 2nd solvent species. Even when the solvent is not a mixed one and the number of solvent species is unity, the second column is present and is equal to 1.
+The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the first and second  columns and have the pair energy within the mesh specified i those columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
+The fifth column is the density (i.e. the value in the fourth column / bin width).
+
+
+**On Version 0.3 or below**, the format is:

 ~~~~
 ...
@@ -18,32 +38,9 @@
 ...
 ~~~~

-The first column in each line corresponds to the discretized, pair energy between solute and solvent and is the mid-point energy of the mesh.
-To be more precise, it is the mid-point energy of the mesh when the energy is smaller than eccore described in [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03), and is the geometric mean of the end values of the mesh when the energy is larger than eccore.
-
-The second column in each line identifies the solvent species.
-When its value is 2, for example, the line refers to the pair energy between the solute and the 2nd solvent species.
-Even when the solvent is not a mixed one and the number of solvent species is unity, the second column is present and is equal to 1.
-
-The third column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the second column and have the pair energy within the mesh specified by the first column.
-
+The first, second, and third columns correspond to the second, third, and fourth columns in the above, respectively.
 It should be noted that the third column is the average histogram, not the density.
 To determine the pair-energy density, the value at the third column needs to be divided by the width of the corresponding mesh.
-Since the third column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
-
-**After version 1.0,**  a new format was introduced:
-
-~~~~
-...
-  -4.370000      -4.345000        1    0.350465725129100E-01    0.700931450258191
-  -4.320000      -4.295000        1    0.380929927424355E-01    0.761859854848727
-  -4.270000      -4.245000        1    0.339955644632201E-01    0.679911289264393
-  -4.220000      -4.195000        1    0.429572985100842E-01    0.859145970201672
-  -4.170000      -4.145000        1    0.300335490894311E-01    0.600670981788636
-...
-~~~~
-
-The first column is the beginning of the energy bin (smallest energy of the bin). The second column is the middle point (arithmetic or geometric mean of the first column and that of the next line) of the bin. Third column is the solvent species. The fourth column is the average histogram, and the fifth column is the density (i.e. fourth column / bin width). 

 engref.XX and corref.XX
 ----
@@ -64,7 +61,7 @@

 aveuv.tt is an output only in a soln run.
 It provides the average sum of the solute-solvent interaction energy in each block of the MD trajectory in soln.
-As described in [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03), the MD trajectory in soln is divided in into a certain number of blocks specified by engdiv, and the average sum is given for each block.
+As described in  [Parameter files for erdst](parameters-erdst), the MD trajectory in soln is divided in into a certain number of blocks specified by engdiv, and the average sum is given for each block.
 Typically, aveuv.tt reads like

 ~~~~
@@ -111,7 +108,7 @@
 ----

 uvrange.tt is an output both in soln and refs runs, and provides the minimum and maximum values of the interaction energy of the solute with each solvent species.
-This file is generated when the ermod program finishes successfully.
+This file is generated when the erdst program finishes successfully.
 A uvrange.tt output looks like

 ~~~~
@@ -140,10 +137,10 @@
 ----

 weight_soln is an output in a soln run and weight_refs is an output in a refs run.
-They give the statistical weight for each block of the MD trajectory; the number of blocks is specified by engdiv described in [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03).
+They give the statistical weight for each block of the MD trajectory; the number of blocks is specified by engdiv described in  [Parameter files for erdst](parameters-erdst).
 When some average is to be taken over the blocks, the weights provided in weight_soln or weight_refs are assigned to the blocks.

-There are two formats of output depending on the value of wgtslf described in [Parameter files for ermod (ver 0.2)](parameters-ermod02) or [Parameter files for ermod (ver 0.3)](parameters-ermod03).
+There are two formats of output depending on the value of wgtslf described in [Parameter files for erdst](parameters-erdst).
 When wgtslf = 0 (default setting in a soln calculation and in a refs calculation without the Ewald or PME method), the typical output looks like

 ~~~~

output modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 03:51:48 -0000

--- v23
+++ v24
@@ -6,7 +6,7 @@

 engsln.XX is an output only in a soln run.
 This output file is an input to the slvfe program to compute the solvation free energy.
-engsln.XX typically reads like on Version 0.3 or below:
+engsln.XX typically reads like **on Version 0.3 or below:**

 ~~~~
 ...
@@ -31,7 +31,7 @@
 To determine the pair-energy density, the value at the third column needs to be divided by the width of the corresponding mesh.
 Since the third column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.

-After version 1.0,  a new format was introduced:
+**After version 1.0,**  a new format was introduced:

 ~~~~
 ...

output modified by Shun Sakuraba

Shun Sakuraba — Thu, 11 Apr 2024 03:51:26 -0000

--- v22
+++ v23
@@ -6,7 +6,7 @@

 engsln.XX is an output only in a soln run.
 This output file is an input to the slvfe program to compute the solvation free energy.
-engsln.XX typically reads like
+engsln.XX typically reads like on Version 0.3 or below:

 ~~~~
 ...
@@ -31,6 +31,19 @@
 To determine the pair-energy density, the value at the third column needs to be divided by the width of the corresponding mesh.
 Since the third column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.

+After version 1.0,  a new format was introduced:
+
+~~~~
+...
+  -4.370000      -4.345000        1    0.350465725129100E-01    0.700931450258191
+  -4.320000      -4.295000        1    0.380929927424355E-01    0.761859854848727
+  -4.270000      -4.245000        1    0.339955644632201E-01    0.679911289264393
+  -4.220000      -4.195000        1    0.429572985100842E-01    0.859145970201672
+  -4.170000      -4.145000        1    0.300335490894311E-01    0.600670981788636
+...
+~~~~
+
+The first column is the beginning of the energy bin (smallest energy of the bin). The second column is the middle point (arithmetic or geometric mean of the first column and that of the next line) of the bin. Third column is the solvent species. The fourth column is the average histogram, and the fifth column is the density (i.e. fourth column / bin width). 

 engref.XX and corref.XX
 ----