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Added names of action in value dictionary that is output by driver an…
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…d used by PlumedToHTML

This commit looks more complicated as for actions like DISTANCE_VECTOR I want the name
of the action to be displayed as DISTANCE as that is the name the user employs.  I achieve
this by setting a display name for each action in the keywords file.
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Gareth Aneurin Tribello authored and Gareth Aneurin Tribello committed May 17, 2024
1 parent 0ac7ea7 commit 8e9a99c
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Showing 39 changed files with 175 additions and 61 deletions.
10 changes: 10 additions & 0 deletions regtest/basic/rt-parse-only/values.json.reference
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Original file line number Diff line number Diff line change
@@ -1,32 +1,42 @@
{
"timestep" : {
"action" : "PUT",
"timestep" : { "type": "scalar", "desciption": "" }
},
"posx" : {
"action" : "PUT",
"posx" : { "type": "vector", "desciption": "" }
},
"posy" : {
"action" : "PUT",
"posy" : { "type": "vector", "desciption": "" }
},
"posz" : {
"action" : "PUT",
"posz" : { "type": "vector", "desciption": "" }
},
"Masses" : {
"action" : "PUT",
"Masses" : { "type": "vector", "desciption": "" }
},
"Charges" : {
"action" : "PUT",
"Charges" : { "type": "vector", "desciption": "" }
},
"Box" : {
"action" : "PBC",
"Box" : { "type": "matrix", "desciption": "" }
},
"phi" : {
"action" : "TORSION",
"phi" : { "type": "scalar", "desciption": "" }
},
"r1" : {
"action" : "READ",
"r1.X" : { "type": "scalar", "description": "values from the column labelled p2.X in the file named input_colvar" }
},
"r2" : {
"action" : "READ",
"r2.X" : { "type": "scalar", "description": "values from the column labelled p3.X in the file named input_colvar" },
"r2.Y" : { "type": "scalar", "description": "values from the column labelled p3.Y in the file named input_colvar" },
"r2.zzz" : { "type": "scalar", "description": "values from the column labelled p3.zzz in the file named input_colvar" }
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31 changes: 31 additions & 0 deletions regtest/contour/rt-parse-only/values.json.reference
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Original file line number Diff line number Diff line change
@@ -1,102 +1,133 @@
{
"timestep" : {
"action" : "PUT",
"timestep" : { "type": "scalar", "desciption": "" }
},
"posx" : {
"action" : "PUT",
"posx" : { "type": "vector", "desciption": "" }
},
"posy" : {
"action" : "PUT",
"posy" : { "type": "vector", "desciption": "" }
},
"posz" : {
"action" : "PUT",
"posz" : { "type": "vector", "desciption": "" }
},
"Masses" : {
"action" : "PUT",
"Masses" : { "type": "vector", "desciption": "" }
},
"Charges" : {
"action" : "PUT",
"Charges" : { "type": "vector", "desciption": "" }
},
"Box" : {
"action" : "PBC",
"Box" : { "type": "matrix", "desciption": "" }
},
"fcc_grp" : {
"action" : "GROUP",
"fcc_grp" : { "type": "atoms", "desciption": "" }
},
"fcc_mat" : {
"action" : "CONTACT_MATRIX",
"fcc_mat.w" : { "type": "matrix", "desciption": "" }
"fcc_mat.x" : { "type": "matrix", "desciption": "" }
"fcc_mat.y" : { "type": "matrix", "desciption": "" }
"fcc_mat.z" : { "type": "matrix", "desciption": "" }
},
"fcc_vfunc" : {
"action" : "FCCUBIC_FUNC",
"fcc_vfunc" : { "type": "matrix", "desciption": "" }
},
"fcc_wvfunc" : {
"action" : "CUSTOM",
"fcc_wvfunc" : { "type": "matrix", "desciption": "" }
},
"fcc_ones" : {
"action" : "CONSTANT",
"fcc_ones" : { "type": "vector", "desciption": "" }
},
"shortcut_fcc_ones" : {
"action" : "ONES",
"fcc_ones" : { "type": "vector", "desciption": "" }
},
"fcc" : {
"action" : "MATRIX_VECTOR_PRODUCT",
"fcc" : { "type": "vector", "desciption": "" }
},
"fcc_denom" : {
"action" : "MATRIX_VECTOR_PRODUCT",
"fcc_denom" : { "type": "vector", "desciption": "" }
},
"fcc_n" : {
"action" : "CUSTOM",
"fcc_n" : { "type": "vector", "desciption": "" }
},
"shortcut_fcc" : {
"action" : "FCCUBIC",
"fcc" : { "type": "vector", "desciption": "" }
},
"dens_dist" : {
"action" : "DISTANCE",
"dens_dist.x" : { "type": "vector", "desciption": "" }
"dens_dist.y" : { "type": "vector", "desciption": "" }
"dens_dist.z" : { "type": "vector", "desciption": "" }
},
"shortcut_dens_dist" : {
"action" : "DISTANCES",
"dens_dist.x" : { "type": "vector", "desciption": "" }
"dens_dist.y" : { "type": "vector", "desciption": "" }
"dens_dist.z" : { "type": "vector", "desciption": "" }
},
"dens_numer_sigma" : {
"action" : "CONSTANT",
"dens_numer_sigma" : { "type": "vector", "desciption": "" }
},
"dens_numer_cov" : {
"action" : "CUSTOM",
"dens_numer_cov" : { "type": "vector", "desciption": "" }
},
"dens_numer_icov" : {
"action" : "CUSTOM",
"dens_numer_icov" : { "type": "vector", "desciption": "" }
},
"dens_numer" : {
"action" : "KDE",
"dens_numer" : { "type": "grid", "desciption": "" }
},
"ones" : {
"action" : "CONSTANT",
"ones" : { "type": "vector", "desciption": "" }
},
"shortcut_ones" : {
"action" : "ONES",
"ones" : { "type": "vector", "desciption": "" }
},
"dens_denom_sigma" : {
"action" : "CONSTANT",
"dens_denom_sigma" : { "type": "vector", "desciption": "" }
},
"dens_denom_cov" : {
"action" : "CUSTOM",
"dens_denom_cov" : { "type": "vector", "desciption": "" }
},
"dens_denom_icov" : {
"action" : "CUSTOM",
"dens_denom_icov" : { "type": "vector", "desciption": "" }
},
"dens_denom" : {
"action" : "KDE",
"dens_denom" : { "type": "grid", "desciption": "" }
},
"dens" : {
"action" : "CUSTOM",
"dens" : { "type": "grid", "desciption": "" }
},
"cont" : {
"action" : "FIND_CONTOUR",
"cont.dens_dist.x" : { "type": "vector", "description": "a vector of coordinates for the contour along the dens_dist.x direction" },
"cont.dens_dist.y" : { "type": "vector", "description": "a vector of coordinates for the contour along the dens_dist.y direction" },
"cont.dens_dist.z" : { "type": "vector", "description": "a vector of coordinates for the contour along the dens_dist.z direction" }
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27 changes: 27 additions & 0 deletions regtest/multicolvar/rt-parse-only/values.json.reference
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Original file line number Diff line number Diff line change
@@ -1,88 +1,115 @@
{
"timestep" : {
"action" : "PUT",
"timestep" : { "type": "scalar", "desciption": "" }
},
"posx" : {
"action" : "PUT",
"posx" : { "type": "vector", "desciption": "" }
},
"posy" : {
"action" : "PUT",
"posy" : { "type": "vector", "desciption": "" }
},
"posz" : {
"action" : "PUT",
"posz" : { "type": "vector", "desciption": "" }
},
"Masses" : {
"action" : "PUT",
"Masses" : { "type": "vector", "desciption": "" }
},
"Charges" : {
"action" : "PUT",
"Charges" : { "type": "vector", "desciption": "" }
},
"Box" : {
"action" : "PBC",
"Box" : { "type": "matrix", "desciption": "" }
},
"d1" : {
"action" : "DISTANCE",
"d1" : { "type": "scalar", "desciption": "" }
},
"d2" : {
"action" : "DISTANCE",
"d2" : { "type": "scalar", "desciption": "" }
},
"d3" : {
"action" : "DISTANCE",
"d3" : { "type": "scalar", "desciption": "" }
},
"ss" : {
"action" : "SORT",
"ss.1" : { "type": "scalar", "desciption": "1th" }
"ss.2" : { "type": "scalar", "desciption": "2th" }
"ss.3" : { "type": "scalar", "desciption": "3th" }
},
"dall" : {
"action" : "DISTANCE",
"dall" : { "type": "vector", "desciption": "" }
},
"ssall" : {
"action" : "SORT",
"ssall.1" : { "type": "scalar", "desciption": "1th" }
"ssall.2" : { "type": "scalar", "desciption": "2th" }
"ssall.3" : { "type": "scalar", "desciption": "3th" }
},
"dallt" : {
"action" : "DISTANCE",
"dallt" : { "type": "vector", "desciption": "" }
},
"sfinal" : {
"action" : "SORT",
"sfinal.1" : { "type": "scalar", "desciption": "1th" }
"sfinal.2" : { "type": "scalar", "desciption": "2th" }
},
"dallk_vatom1" : {
"action" : "CENTER_FAST",
"dallk_vatom1" : { "type": "atoms", "desciption": "" }
},
"dallk_vatom2" : {
"action" : "CENTER_FAST",
"dallk_vatom2" : { "type": "atoms", "desciption": "" }
},
"dallk_vatom3" : {
"action" : "CENTER_FAST",
"dallk_vatom3" : { "type": "atoms", "desciption": "" }
},
"dallk_grp" : {
"action" : "GROUP",
"dallk_grp" : { "type": "atoms", "desciption": "" }
},
"dallk" : {
"action" : "DISTANCE",
"dallk" : { "type": "vector", "desciption": "" }
},
"dallk_lt1" : {
"action" : "LESS_THAN",
"dallk_lt1" : { "type": "vector", "desciption": "" }
},
"dallk_lessthan-1" : {
"action" : "SUM",
"dallk_lessthan-1" : { "type": "scalar", "desciption": "" }
},
"dallk_lt2" : {
"action" : "LESS_THAN",
"dallk_lt2" : { "type": "vector", "desciption": "" }
},
"dallk_lessthan-2" : {
"action" : "SUM",
"dallk_lessthan-2" : { "type": "scalar", "desciption": "" }
},
"dallk_lowest" : {
"action" : "LOWEST",
"dallk_lowest" : { "type": "scalar", "desciption": "" }
},
"dallk_mean" : {
"action" : "MEAN",
"dallk_mean" : { "type": "scalar", "desciption": "" }
},
"shortcut_dallk" : {
"action" : "DISTANCES",
"dallk" : { "type": "vector", "desciption": "" }
"dallk_lessthan-1" : { "type": "scalar", "desciption": "" }
"dallk_lessthan-2" : { "type": "scalar", "desciption": "" }
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19 changes: 19 additions & 0 deletions regtest/symfunc/rt-parse-only/values.json.reference
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Original file line number Diff line number Diff line change
@@ -1,35 +1,45 @@
{
"timestep" : {
"action" : "PUT",
"timestep" : { "type": "scalar", "desciption": "" }
},
"posx" : {
"action" : "PUT",
"posx" : { "type": "vector", "desciption": "" }
},
"posy" : {
"action" : "PUT",
"posy" : { "type": "vector", "desciption": "" }
},
"posz" : {
"action" : "PUT",
"posz" : { "type": "vector", "desciption": "" }
},
"Masses" : {
"action" : "PUT",
"Masses" : { "type": "vector", "desciption": "" }
},
"Charges" : {
"action" : "PUT",
"Charges" : { "type": "vector", "desciption": "" }
},
"Box" : {
"action" : "PBC",
"Box" : { "type": "matrix", "desciption": "" }
},
"q1_grp" : {
"action" : "GROUP",
"q1_grp" : { "type": "atoms", "desciption": "" }
},
"q1_mat" : {
"action" : "CONTACT_MATRIX",
"q1_mat.w" : { "type": "matrix", "desciption": "" }
"q1_mat.x" : { "type": "matrix", "desciption": "" }
"q1_mat.y" : { "type": "matrix", "desciption": "" }
"q1_mat.z" : { "type": "matrix", "desciption": "" }
},
"q1_sh" : {
"action" : "SPHERICAL_HARMONIC",
"q1_sh.rm-n1" : { "type": "matrix", "desciption": "" }
"q1_sh.rm-0" : { "type": "matrix", "desciption": "" }
"q1_sh.rm-p1" : { "type": "matrix", "desciption": "" }
Expand All @@ -38,15 +48,19 @@
"q1_sh.im-p1" : { "type": "matrix", "desciption": "" }
},
"q1_denom_ones" : {
"action" : "CONSTANT",
"q1_denom_ones" : { "type": "vector", "desciption": "" }
},
"shortcut_q1_denom_ones" : {
"action" : "ONES",
"q1_denom_ones" : { "type": "vector", "desciption": "" }
},
"q1_denom" : {
"action" : "MATRIX_VECTOR_PRODUCT",
"q1_denom" : { "type": "vector", "desciption": "" }
},
"q1_sp" : {
"action" : "MATRIX_VECTOR_PRODUCT",
"q1_sp.rm-n1" : { "type": "vector", "description": "the product of the matrix q1_sh.rm-n1 and the vector q1_denom_ones" },
"q1_sp.rm-0" : { "type": "vector", "description": "the product of the matrix q1_sh.rm-0 and the vector q1_denom_ones" },
"q1_sp.rm-p1" : { "type": "vector", "description": "the product of the matrix q1_sh.rm-p1 and the vector q1_denom_ones" },
Expand All @@ -55,18 +69,23 @@
"q1_sp.im-p1" : { "type": "vector", "description": "the product of the matrix q1_sh.im-p1 and the vector q1_denom_ones" }
},
"q1_norm2" : {
"action" : "COMBINE",
"q1_norm2" : { "type": "vector", "desciption": "" }
},
"q1_norm" : {
"action" : "CUSTOM",
"q1_norm" : { "type": "vector", "desciption": "" }
},
"q1" : {
"action" : "CUSTOM",
"q1" : { "type": "vector", "desciption": "" }
},
"shortcut_q1" : {
"action" : "Q1",
"q1" : { "type": "vector", "desciption": "" }
},
"gg" : {
"action" : "GSYMFUNC_THREEBODY",
"gg.g6" : { "type": "vector", "description": "the function defined by the FUNCTION1 keyword" },
"gg.g7" : { "type": "vector", "description": "the function defined by the FUNCTION2 keyword" }
}
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Found broken examples in automatic/ANGLES.tmp
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