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Merge pull request #3790 from jrgissing/is_typelabel-function

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add is_typelabel() variable function
This commit is contained in:
Axel Kohlmeyer
2023-05-31 15:15:08 -04:00
committed by GitHub
parent 2a799d45a9 4073241413
commit 5f8b0f56a5
3 changed files with 77 additions and 22 deletions
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19
doc/src/variable.rst
View File

@ -67,7 +67,7 @@ Syntax
bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label)
feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
@ -532,7 +532,7 @@ variables.
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label) |
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) |
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@ -996,10 +996,17 @@ via the link in this paragraph.
The label2type(kind,label) function converts type labels into numeric
types, using label maps created by the :doc:`labelmap <labelmap>` or
:doc:`read_data <read_data>` commands. The first argument is the
label map kind (atom, bond, angle, dihedral, or improper) and the
second argument is the label. The function returns the corresponding
numeric type.
:doc:`read_data <read_data>` commands. The first argument is the label
map kind (atom, bond, angle, dihedral, or improper) and the second
argument is the label. The function returns the corresponding numeric
type or triggers an error if the queried label does not exist.
.. versionadded:: TBD
The is_typelabel(kind,label) function has the same arguments as
label2type(), but returns 1 if the type label has been assigned,
otherwise it returns 0. This function can be used to check if a
particular type label already exists in the simulation.
----------

34
src/variable.cpp
View File

@ -4040,8 +4040,8 @@ Region *Variable::region_function(char *id, int ivar)
return 0 if not a match, 1 if successfully processed
customize by adding a special function:
sum(x),min(x),max(x),ave(x),trap(x),slope(x),
gmask(x),rmask(x),grmask(x,y),next(x),
is_file(x),is_ox(x),extract_setting(x),label2type(x,y)
gmask(x),rmask(x),grmask(x,y),next(x),is_file(x),is_ox(x),
extract_setting(x),label2type(x,y),is_typelabel(x,y)
------------------------------------------------------------------------- */
int Variable::special_function(char *word, char *contents, Tree **tree, Tree **treestack,
@ -4056,20 +4056,28 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
strcmp(word,"ave") != 0 && strcmp(word,"trap") != 0 && strcmp(word,"slope") != 0 &&
strcmp(word,"gmask") != 0 && strcmp(word,"rmask") != 0 && strcmp(word,"grmask") != 0 &&
strcmp(word,"next") != 0 && strcmp(word,"is_file") != 0 && strcmp(word,"is_os") != 0 &&
strcmp(word,"extract_setting") != 0 && strcmp(word,"label2type") != 0)
strcmp(word,"extract_setting") != 0 && strcmp(word,"label2type") != 0 &&
strcmp(word,"is_typelabel") != 0)
return 0;
// process label2type() separately b/c its label arg can have commas in it
if (strcmp(word,"label2type") == 0) {
if (strcmp(word,"label2type") == 0 || strcmp(word,"is_typelabel") == 0) {
if (!atom->labelmapflag)
print_var_error(FLERR,"Cannot use label2type() function without a labelmap",ivar);
print_var_error(FLERR,fmt::format("Cannot use {}() function without a labelmap",word),ivar);
std::string contents_copy(contents);
auto pos = contents_copy.find_first_of(',');
if (pos == std::string::npos)
print_var_error(FLERR, fmt::format("Invalid label2type({}) function in variable formula",
contents_copy), ivar);
if (pos == std::string::npos) {
if (strcmp(word,"label2type") == 0) {
print_var_error(FLERR, fmt::format("Invalid label2type({}) function in variable formula",
contents_copy), ivar);
} else {
print_var_error(FLERR, fmt::format("Invalid is_typelabel({}) function in variable formula",
contents_copy), ivar);
}
}
std::string typestr = contents_copy.substr(pos+1);
std::string kind = contents_copy.substr(0, pos);
@ -4085,12 +4093,14 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **t
} else if (kind == "improper") {
value = atom->lmap->find(typestr,Atom::IMPROPER);
} else {
print_var_error(FLERR, fmt::format("Invalid kind {} in label2type() in variable",kind),ivar);
print_var_error(FLERR, fmt::format("Invalid kind {} in {}() in variable", kind, word),ivar);
}
if (value == -1)
print_var_error(FLERR, fmt::format("Invalid {} type label {} in label2type() in variable",
kind, typestr), ivar);
if (strcmp(word,"label2type") == 0) {
if (value == -1)
print_var_error(FLERR, fmt::format("Invalid {} type label {} in label2type() in variable",
kind, typestr), ivar);
} else value = (value == -1) ? 0.0 : 1.0;
// save value in tree or on argstack

46
unittest/commands/test_variables.cpp
View File

@ -590,7 +590,7 @@ TEST_F(VariableTest, NextCommand)
command("next five four"););
}
TEST_F(VariableTest, Label2TypeAtomic)
TEST_F(VariableTest, LabelMapAtomic)
{
BEGIN_HIDE_OUTPUT();
command("region box block 0 2 0 2 0 2");
@ -608,14 +608,20 @@ TEST_F(VariableTest, Label2TypeAtomic)
ASSERT_DOUBLE_EQ(variable->compute_equal("label2type(atom,N1)"), 2.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("label2type(atom,O1)"), 3.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("label2type(atom,H1)"), 4.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(atom,N1)"), 1.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(atom,N2)"), 0.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(atom,O)"), 0.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(atom,H1)"), 1.0);
TEST_FAILURE(".*ERROR: Variable t1: Invalid atom type label C1 in label2type.. in variable.*",
command("print \"${t1}\""););
TEST_FAILURE(".*ERROR: Invalid bond type label H1 in label2type.. in variable.*",
variable->compute_equal("label2type(bond,H1)"););
TEST_FAILURE(".*ERROR: Invalid kind xxx in label2type.. in variable.*",
variable->compute_equal("label2type(xxx,H1)"););
TEST_FAILURE(".*ERROR: Invalid kind xxx in is_typelabel.. in variable.*",
variable->compute_equal("is_typelabel(xxx,H1)"););
}
TEST_F(VariableTest, Label2TypeMolecular)
TEST_F(VariableTest, LabelMapMolecular)
{
if (!info->has_style("atom", "full")) GTEST_SKIP();
@ -637,6 +643,14 @@ TEST_F(VariableTest, Label2TypeMolecular)
command("variable a2 equal \"\"\"label2type(angle,N2'-C1\"-N2')\"\"\"");
command("variable d1 equal label2type(dihedral,C1-N2-C1-N2)");
command("variable i1 equal label2type(improper,C1-N2-C1-N2)");
command("variable l1 equal is_typelabel(atom,C2)+is_typelabel(bond,C2-N1)"
"+is_typelabel(bond,[X1][Y1])+is_typelabel(angle,C1-C2-N1)"
"+is_typelabel(dihedral,N2-C1-C1-N2)+is_typelabel(improper,N2-C1-C1-N2)");
command("variable l2 equal is_typelabel(atom,C1)+is_typelabel(bond,C1-N2)"
"+is_typelabel(bond,[C1][C1])+is_typelabel(angle,C1-N2-C1)"
"+is_typelabel(dihedral,C1-N2-C1-N2)+is_typelabel(improper,C1-N2-C1-N2)");
END_HIDE_OUTPUT();
ASSERT_THAT(variable->retrieve("t1"), StrEq("1"));
@ -647,6 +661,30 @@ TEST_F(VariableTest, Label2TypeMolecular)
ASSERT_THAT(variable->retrieve("a2"), StrEq("2"));
ASSERT_THAT(variable->retrieve("d1"), StrEq("1"));
ASSERT_THAT(variable->retrieve("i1"), StrEq("1"));
ASSERT_THAT(variable->retrieve("l1"), StrEq("0"));
ASSERT_THAT(variable->retrieve("l2"), StrEq("6"));
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(atom,N2')"), 1.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(atom,\"N2'\")"), 0.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(bond,C1-N2)"), 1.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(bond,C2-N1)"), 0.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(bond,[C1][C1])"), 1.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(bond,[X1][Y1])"), 0.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(angle,C1-C2-N1)"), 0.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(angle,C1-N2-C1)"), 1.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(dihedral,C1-N2-C1-N2)"), 1.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(dihedral,N2-C1-C1-N2)"), 0.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(improper,C1-N2-C1-N2)"), 1.0);
ASSERT_DOUBLE_EQ(variable->compute_equal("is_typelabel(improper,N2-C1-C1-N2)"), 0.0);
TEST_FAILURE(".*ERROR: Invalid bond type label H1 in label2type.. in variable.*",
variable->compute_equal("label2type(bond,H1)"););
TEST_FAILURE(".*ERROR: Invalid angle type label H1 in label2type.. in variable.*",
variable->compute_equal("label2type(angle,H1)"););
TEST_FAILURE(".*ERROR: Invalid dihedral type label H1 in label2type.. in variable.*",
variable->compute_equal("label2type(dihedral,H1)"););
TEST_FAILURE(".*ERROR: Invalid improper type label H1 in label2type.. in variable.*",
variable->compute_equal("label2type(improper,H1)"););
}
TEST_F(VariableTest, Format)