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Merge branch 'lammps:develop' into local-composition

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This commit is contained in:
Megan J. McCarthy (Meg)
2023-06-01 07:46:15 -06:00
committed by GitHub
parent 9a389fbac6 5f8b0f56a5
commit 0e4d5f03a1
10 changed files with 1932 additions and 22 deletions
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19
doc/src/variable.rst
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@ -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.
----------

1
examples/snap/C_SNAP_2021.10.15.quadratic.snapcoeff Symbolic link
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../../potentials/C_SNAP_2021.10.15.quadratic.snapcoeff

1
examples/snap/C_SNAP_2021.10.15.quadratic.snapparam Symbolic link
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@ -0,0 +1 @@
../../potentials/C_SNAP_2021.10.15.quadratic.snapparam

31
examples/snap/in.C_SNAP Normal file
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@ -0,0 +1,31 @@
#Carbon SNAP example: 216 atom diamond unit cell simulated NVT at ~1,000GPa and 5,000K
units metal
atom_style atomic
boundary p p p
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Crystal orientation and MD box creation #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
lattice diamond 2.845
region Bbox block 0 3 0 3 0 3
create_box 1 Bbox
create_atoms 1 region Bbox basis 1 1
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Interatomic potential parameters #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
pair_style hybrid/overlay zbl 0.1 0.2 snap
pair_coeff 1 1 zbl 10 10
pair_coeff * * snap C_SNAP_2021.10.15.quadratic.snapcoeff C_SNAP_2021.10.15.quadratic.snapparam C
mass * 12.01
velocity all create 8000.0 3412461 loop geom
fix NVE all nve
fix NVT all langevin 5000.0 5000.0 0.1 3216548
thermo 50
thermo_style custom step temp ke pe etotal press pxx pyy pzz
run 500

105
examples/snap/log.30May23.C_SNAP.g++.1 Normal file
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@ -0,0 +1,105 @@
LAMMPS (28 Mar 2023 - Development)
using 1 OpenMP thread(s) per MPI task
#Carbon SNAP example: 216 atom diamond unit cell simulated NVT at ~1,000GPa and 5,000K
units metal
atom_style atomic
boundary p p p
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Crystal orientation and MD box creation #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
lattice diamond 2.845
Lattice spacing in x,y,z = 2.845 2.845 2.845
region Bbox block 0 3 0 3 0 3
create_box 1 Bbox
Created orthogonal box = (0 0 0) to (8.535 8.535 8.535)
1 by 1 by 1 MPI processor grid
create_atoms 1 region Bbox basis 1 1
Created 216 atoms
using lattice units in orthogonal box = (0 0 0) to (8.535 8.535 8.535)
create_atoms CPU = 0.000 seconds
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Interatomic potential parameters #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
pair_style hybrid/overlay zbl 0.1 0.2 snap
pair_coeff 1 1 zbl 10 10
pair_coeff * * snap C_SNAP_2021.10.15.quadratic.snapcoeff C_SNAP_2021.10.15.quadratic.snapparam C
SNAP Element = C, Radius 0.5, Weight 1
SNAP keyword rcutfac 2.7
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0.0
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 1
mass * 12.01
velocity all create 8000.0 3412461 loop geom
fix NVE all nve
fix NVT all langevin 5000.0 5000.0 0.1 3216548
thermo 50
thermo_style custom step temp ke pe etotal press pxx pyy pzz
run 500
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.7
ghost atom cutoff = 4.7
binsize = 2.35, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair zbl, perpetual, half/full trim from (2)
attributes: half, newton on, cut 2.2
pair build: halffull/newton/trim
stencil: none
bin: none
(2) pair snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.835 | 4.835 | 4.835 Mbytes
Step Temp KinEng PotEng TotEng Press Pxx Pyy Pzz
0 8000 222.32745 -846.66062 -624.33318 10234249 10210805 10267435 10224506
50 4199.4229 116.70587 -723.2423 -606.53643 10256033 10157803 10280166 10330129
100 3820.2509 106.16833 -710.43537 -604.26704 10232872 10216484 10241309 10240825
150 4413.2948 122.64957 -710.09702 -587.44745 10254093 10323013 10265454 10173810
200 4688.024 130.28455 -702.26198 -571.97742 10306186 10281632 10342390 10294536
250 4997.165 138.87587 -720.58476 -581.70889 10284438 10220856 10360231 10272226
300 4640.4911 128.96357 -710.75063 -581.78706 10263301 10264007 10290526 10235369
350 4929.5117 136.99572 -707.2526 -570.25688 10290742 10359920 10284236 10228071
400 4700.9354 130.64337 -697.90277 -567.2594 10250682 10277287 10246032 10228729
450 5108.4971 141.96989 -700.57144 -558.60155 10289765 10323648 10306588 10239058
500 5146.7039 143.03169 -700.33221 -557.30052 10334303 10349736 10358785 10294387
Loop time of 36.7771 on 1 procs for 500 steps with 216 atoms
Performance: 1.175 ns/day, 20.432 hours/ns, 13.595 timesteps/s, 2.937 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 36.766 | 36.766 | 36.766 | 0.0 | 99.97
Neigh | 0.0010226 | 0.0010226 | 0.0010226 | 0.0 | 0.00
Comm | 0.0033205 | 0.0033205 | 0.0033205 | 0.0 | 0.01
Output | 0.00020657 | 0.00020657 | 0.00020657 | 0.0 | 0.00
Modify | 0.0047621 | 0.0047621 | 0.0047621 | 0.0 | 0.01
Other | | 0.001464 | | | 0.00
Nlocal: 216 ave 216 max 216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1746 ave 1746 max 1746 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1767 ave 1767 max 1767 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 32846 ave 32846 max 32846 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 32846
Ave neighs/atom = 152.06481
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:36

105
examples/snap/log.30May23.C_SNAP.g++.4 Normal file
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@ -0,0 +1,105 @@
LAMMPS (28 Mar 2023 - Development)
using 1 OpenMP thread(s) per MPI task
#Carbon SNAP example: 216 atom diamond unit cell simulated NVT at ~1,000GPa and 5,000K
units metal
atom_style atomic
boundary p p p
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Crystal orientation and MD box creation #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
lattice diamond 2.845
Lattice spacing in x,y,z = 2.845 2.845 2.845
region Bbox block 0 3 0 3 0 3
create_box 1 Bbox
Created orthogonal box = (0 0 0) to (8.535 8.535 8.535)
1 by 2 by 2 MPI processor grid
create_atoms 1 region Bbox basis 1 1
Created 216 atoms
using lattice units in orthogonal box = (0 0 0) to (8.535 8.535 8.535)
create_atoms CPU = 0.000 seconds
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Interatomic potential parameters #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
pair_style hybrid/overlay zbl 0.1 0.2 snap
pair_coeff 1 1 zbl 10 10
pair_coeff * * snap C_SNAP_2021.10.15.quadratic.snapcoeff C_SNAP_2021.10.15.quadratic.snapparam C
SNAP Element = C, Radius 0.5, Weight 1
SNAP keyword rcutfac 2.7
SNAP keyword twojmax 8
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0.0
SNAP keyword bzeroflag 0
SNAP keyword quadraticflag 1
mass * 12.01
velocity all create 8000.0 3412461 loop geom
fix NVE all nve
fix NVT all langevin 5000.0 5000.0 0.1 3216548
thermo 50
thermo_style custom step temp ke pe etotal press pxx pyy pzz
run 500
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.7
ghost atom cutoff = 4.7
binsize = 2.35, bins = 4 4 4
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair zbl, perpetual, half/full trim from (2)
attributes: half, newton on, cut 2.2
pair build: halffull/newton/trim
stencil: none
bin: none
(2) pair snap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.681 | 4.681 Mbytes
Step Temp KinEng PotEng TotEng Press Pxx Pyy Pzz
0 8000 222.32745 -846.66062 -624.33318 10234249 10210805 10267435 10224506
50 4382.3571 121.78978 -715.70492 -593.91513 10262157 10278549 10181545 10326376
100 4546.1549 126.34188 -713.11818 -586.77631 10261694 10257647 10333666 10193770
150 5109.4576 141.99658 -708.87952 -566.88294 10268132 10248182 10248240 10307974
200 4764.2181 132.40206 -712.16881 -579.76675 10329903 10238991 10379394 10371323
250 4989.5099 138.66313 -710.39748 -571.73435 10282678 10321057 10274124 10252854
300 4853.3102 134.87801 -699.98167 -565.10366 10343314 10204138 10430172 10395634
350 4788.1153 133.06618 -705.14381 -572.07763 10325571 10312657 10267999 10396058
400 5055.7813 140.50487 -707.38537 -566.8805 10323176 10357258 10310733 10301536
450 5182.3198 144.02149 -695.11614 -551.09465 10345564 10358486 10346325 10331881
500 5311.077 147.59977 -691.32767 -543.7279 10308823 10242668 10214102 10469700
Loop time of 11.5932 on 4 procs for 500 steps with 216 atoms
Performance: 3.726 ns/day, 6.441 hours/ns, 43.129 timesteps/s, 9.316 katom-step/s
94.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.241 | 10.446 | 10.695 | 5.0 | 90.11
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.87613 | 1.1187 | 1.3179 | 14.9 | 9.65
Output | 0.0002656 | 0.0010016 | 0.0015521 | 1.5 | 0.01
Modify | 0.0019493 | 0.0020668 | 0.0021577 | 0.2 | 0.02
Other | | 0.02508 | | | 0.22
Nlocal: 54 ave 54 max 54 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1082 ave 1082 max 1082 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 432 ave 432 max 432 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 8532 ave 8532 max 8532 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 34128
Ave neighs/atom = 158
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:11

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potentials/C_SNAP_2021.10.15.quadratic.snapcoeff Normal file
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10
potentials/C_SNAP_2021.10.15.quadratic.snapparam Normal file
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@ -0,0 +1,10 @@
# required
rcutfac 2.7
twojmax 8
# optional
rfac0 0.99363
rmin0 0.0
bzeroflag 0
quadraticflag 1

34
src/variable.cpp
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@ -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
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@ -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)