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Merge branch 'python_and_library_fixes' of github.com:rbberger/lammps into python_and_library_fixes

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This commit is contained in:
Richard Berger
2023-06-11 17:48:26 -06:00
parent 68a73f1c33 92e069b19d
commit bc87c69d60
13 changed files with 214 additions and 42 deletions
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5
examples/COUPLE/plugin/liblammpsplugin.h
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@ -37,12 +37,13 @@
#endif
/* The following enums must be kept in sync with the equivalent enums
* or constants in python/lammps/constants.py, fortran/lammps.f90,
* tools/swig/lammps.i, and examples/COUPLE/plugin/liblammpsplugin.h */
* or constants in src/library.h, src/lmptype.h, python/lammps/constants.py,
* fortran/lammps.f90, and tools/swig/lammps.i */
/* Data type constants for extracting data from atoms, computes and fixes */
enum _LMP_DATATYPE_CONST {
LAMMPS_NONE = -1, /*!< no data type assigned (yet) */
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */

11
fortran/lammps.f90
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@ -44,11 +44,12 @@ MODULE LIBLAMMPS
! Data type constants for extracting data from global, atom, compute, and fix
!
! Must be kept in sync with the equivalent declarations in
! src/library.h, python/lammps/constants.py, tools/swig/lammps.i,
! src/library.h, src/lmptype.h, python/lammps/constants.py, tools/swig/lammps.i,
! and examples/COUPLE/plugin/liblammpsplugin.h
!
! These are NOT part of the API (the part the user sees)
INTEGER(c_int), PARAMETER :: &
LAMMPS_NONE = -1, & ! no data type assigned (yet)
LAMMPS_INT = 0, & ! 32-bit integer (or array)
LAMMPS_INT_2D = 1, & ! two-dimensional 32-bit integer array
LAMMPS_DOUBLE = 2, & ! 64-bit double (or array)
@ -1126,11 +1127,13 @@ CONTAINS
FUNCTION lmp_last_thermo(self,what,index) RESULT(thermo_data)
CLASS(lammps), INTENT(IN), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: what
INTEGER(c_int) :: index
INTEGER :: index
INTEGER(c_int) :: idx
TYPE(lammps_data) :: thermo_data, type_data
INTEGER(c_int) :: datatype
TYPE(c_ptr) :: Cname, Cptr
idx = index - 1
! set data type for known cases
SELECT CASE (what)
CASE ('step')
@ -1147,7 +1150,7 @@ CONTAINS
datatype = LAMMPS_STRING
CASE ('data')
Cname = f2c_string('type')
Cptr = lammps_last_thermo(self%handle,Cname,index-1)
Cptr = lammps_last_thermo(self%handle,Cname,idx)
type_data%lammps_instance => self
type_data%datatype = DATA_INT
CALL C_F_POINTER(Cptr, type_data%i32)
@ -1158,7 +1161,7 @@ CONTAINS
END SELECT
Cname = f2c_string(what)
Cptr = lammps_last_thermo(self%handle,Cname,index-1)
Cptr = lammps_last_thermo(self%handle,Cname,idx)
CALL lammps_free(Cname)
thermo_data%lammps_instance => self

8
python/lammps/constants.py
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@ -13,7 +13,13 @@
# various symbolic constants to be used
# in certain calls to select data formats
# these must be kept in sync with the enums in src/library.h, src/lmptype.h,
# tools/swig/lammps.i, examples/COUPLE/plugin/liblammpsplugin.h,
# and the constants in fortran/lammps.f90
LAMMPS_AUTODETECT = None
LAMMPS_NONE = -1
LAMMPS_INT = 0
LAMMPS_INT_2D = 1
LAMMPS_DOUBLE = 2
@ -22,8 +28,6 @@ LAMMPS_INT64 = 4
LAMMPS_INT64_2D = 5
LAMMPS_STRING = 6
# these must be kept in sync with the enums in src/library.h, tools/swig/lammps.i,
# examples/COUPLE/plugin/liblammpsplugin.h, and the constants in fortran/lammps.f90
LMP_STYLE_GLOBAL = 0
LMP_STYLE_ATOM = 1
LMP_STYLE_LOCAL = 2

6
src/EXTRA-DUMP/dump_yaml.cpp
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@ -71,11 +71,11 @@ void DumpYAML::write_header(bigint ndump)
thermo_data += "]\n - data: [ ";
for (int i = 0; i < nfield; ++i) {
if (fields[i].type == multitype::DOUBLE)
if (fields[i].type == multitype::LAMMPS_DOUBLE)
thermo_data += fmt::format("{}, ", fields[i].data.d);
else if (fields[i].type == multitype::INT)
else if (fields[i].type == multitype::LAMMPS_INT)
thermo_data += fmt::format("{}, ", fields[i].data.i);
else if (fields[i].type == multitype::BIGINT)
else if (fields[i].type == multitype::LAMMPS_INT64)
thermo_data += fmt::format("{}, ", fields[i].data.b);
else
thermo_data += ", ";

12
src/NETCDF/dump_netcdf.cpp
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@ -442,11 +442,11 @@ void DumpNetCDF::openfile()
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (fields[i].type == multitype::DOUBLE) {
if (fields[i].type == multitype::LAMMPS_DOUBLE) {
NCERRX( nc_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
} else if (fields[i].type == multitype::LAMMPS_INT) {
NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
} else if (fields[i].type == multitype::LAMMPS_INT64) {
NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
}
}
@ -624,11 +624,11 @@ void DumpNetCDF::write()
int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (filewriter) {
if (fields[i].type == multitype::DOUBLE) {
if (fields[i].type == multitype::LAMMPS_DOUBLE) {
NCERRX( nc_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
} else if (fields[i].type == multitype::LAMMPS_INT) {
NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
} else if (fields[i].type == multitype::LAMMPS_INT64) {
NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
}
}

12
src/NETCDF/dump_netcdf_mpiio.cpp
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@ -432,11 +432,11 @@ void DumpNetCDFMPIIO::openfile()
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (fields[i].type == multitype::DOUBLE) {
if (fields[i].type == multitype::LAMMPS_DOUBLE) {
NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
} else if (fields[i].type == multitype::LAMMPS_INT) {
NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
} else if (fields[i].type == multitype::LAMMPS_INT64) {
NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
}
}
@ -617,11 +617,11 @@ void DumpNetCDFMPIIO::write()
int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (filewriter) {
if (fields[i].type == multitype::DOUBLE) {
if (fields[i].type == multitype::LAMMPS_DOUBLE) {
NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
} else if (fields[i].type == multitype::LAMMPS_INT) {
NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
} else if (fields[i].type == multitype::LAMMPS_INT64) {
NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
}
}

6
src/library.cpp
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@ -836,11 +836,11 @@ void *lammps_last_thermo(void *handle, const char *what, int index)
} else if (strcmp(what, "data") == 0) {
if ((index < 0) || (index >= nfield)) return nullptr;
const auto &field = th->get_fields()[index];
if (field.type == multitype::INT) {
if (field.type == multitype::LAMMPS_INT) {
val = (void *) &field.data.i;
} else if (field.type == multitype::BIGINT) {
} else if (field.type == multitype::LAMMPS_INT64) {
val = (void *) &field.data.b;
} else if (field.type == multitype::DOUBLE) {
} else if (field.type == multitype::LAMMPS_DOUBLE) {
val = (void *) &field.data.d;
}

3
src/library.h
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@ -41,10 +41,11 @@
/** Data type constants for extracting data from atoms, computes and fixes
*
* Must be kept in sync with the equivalent constants in ``python/lammps/constants.py``,
* ``fortran/lammps.f90``, ``tools/swig/lammps.i``, and
* ``fortran/lammps.f90``, ``tools/swig/lammps.i``, ``src/lmptype.h``, and
*``examples/COUPLE/plugin/liblammpsplugin.h`` */
enum _LMP_DATATYPE_CONST {
LAMMPS_NONE = -1, /*!< no data type assigned (yet) */
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */

25
src/lmptype.h
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@ -276,8 +276,21 @@ union ubuf {
\endverbatim
*/
struct multitype {
// same values as LAMMPS_INT, LAMMPS_DOUBLE, and LAMMPS_INT64 in library.h
enum { NONE = -1, INT = 0, DOUBLE = 2, BIGINT = 4 };
/** Data type constants for extracting data from atoms, computes and fixes
*
* This enum must be kept in sync with the corresponding enum or constants
* in ``python/lammps/constants.py``, ``fortran/lammps.f90``, ``tools/swig/lammps.i``,
* ``src/library.h``, and ``examples/COUPLE/plugin/liblammpsplugin.h`` */
enum _LMP_DATATYPE_CONST {
LAMMPS_NONE = -1, /*!< no data type assigned (yet) */
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
LAMMPS_STRING = 6 /*!< C-String */
};
int type;
union {
@ -286,26 +299,26 @@ struct multitype {
int64_t b;
} data;
multitype() : type(NONE) { data.d = 0.0; }
multitype() : type(LAMMPS_NONE) { data.d = 0.0; }
multitype(const multitype &) = default;
multitype(multitype &&) = default;
~multitype() = default;
multitype &operator=(const double &_d)
{
type = DOUBLE;
type = LAMMPS_DOUBLE;
data.d = _d;
return *this;
}
multitype &operator=(const int &_i)
{
type = INT;
type = LAMMPS_INT;
data.i = _i;
return *this;
}
multitype &operator=(const int64_t &_b)
{
type = BIGINT;
type = LAMMPS_INT64;
data.b = _b;
return *this;
}

3
tools/swig/lammps.i
View File

@ -28,9 +28,10 @@
*
* Must be kept in sync with the equivalent constants in ``src/library.h``,
* ``python/lammps/constants.py``, ``examples/COUPLE/plugin/liblammpsplugin.h``,
* and ``fortran/lammps.f90`` */
* ``src/lmptype.h``, and ``fortran/lammps.f90`` */
enum _LMP_DATATYPE_CONST {
LAMMPS_NONE =-1, /*!< no data type assigned (yet) */
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */

108
unittest/fortran/test_fortran_get_thermo.f90
View File

@ -152,3 +152,111 @@ FUNCTION f_lammps_get_thermo_zhi() BIND(C)
f_lammps_get_thermo_zhi = lmp%get_thermo('zhi')
END FUNCTION f_lammps_get_thermo_zhi
SUBROUTINE f_lammps_last_thermo_setup() BIND(C)
USE liblammps
USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input
IMPLICIT NONE
CALL lmp%commands_list(big_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(pair_input)
CALL lmp%command('thermo 10')
CALL lmp%command('run 15 post no')
END SUBROUTINE f_lammps_last_thermo_setup
FUNCTION f_lammps_last_thermo_step() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int, c_int64_t
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_last_thermo_step
INTEGER :: size_bigint
INTEGER(c_int), POINTER :: ival
INTEGER(c_int64_t), POINTER :: bval
size_bigint = lmp%extract_setting('bigint')
IF (size_bigint == 4) THEN
ival = lmp%last_thermo('step',1)
f_lammps_last_thermo_step = INT(ival)
ELSE
bval = lmp%last_thermo('step',1)
f_lammps_last_thermo_step = INT(bval)
END IF
END FUNCTION f_lammps_last_thermo_step
FUNCTION f_lammps_last_thermo_num() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_last_thermo_num
INTEGER(c_int), POINTER :: ival
ival = lmp%last_thermo('num',1)
f_lammps_last_thermo_num = ival
END FUNCTION f_lammps_last_thermo_num
FUNCTION f_lammps_last_thermo_type(idx) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), VALUE :: idx
INTEGER(c_int) :: f_lammps_last_thermo_type
INTEGER(c_int), POINTER :: ival
ival = lmp%last_thermo('type',idx)
f_lammps_last_thermo_type = ival
END FUNCTION f_lammps_last_thermo_type
FUNCTION f_lammps_last_thermo_string(idx) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int, c_ptr, c_null_ptr
USE liblammps
USE keepstuff, ONLY : lmp, f2c_string
IMPLICIT NONE
INTEGER(c_int), VALUE :: idx
TYPE(c_ptr) :: f_lammps_last_thermo_string
CHARACTER(LEN=12) :: buffer
buffer = lmp%last_thermo('keyword',idx)
IF (LEN_TRIM(buffer) > 0) THEN
f_lammps_last_thermo_string = f2c_string(buffer)
ELSE
f_lammps_last_thermo_string = c_null_ptr
END IF
END FUNCTION f_lammps_last_thermo_string
FUNCTION f_lammps_last_thermo_int(idx) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int, c_int64_t
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), VALUE :: idx
INTEGER(c_int), POINTER :: ival
INTEGER(c_int64_t), POINTER :: bval
INTEGER(c_int) :: f_lammps_last_thermo_int
INTEGER :: size_bigint
size_bigint = lmp%extract_setting('bigint')
IF (size_bigint == 4) THEN
ival = lmp%last_thermo('data',idx)
f_lammps_last_thermo_int = INT(ival)
ELSE
bval = lmp%last_thermo('data',idx)
f_lammps_last_thermo_int = INT(bval)
END IF
END FUNCTION f_lammps_last_thermo_int
FUNCTION f_lammps_last_thermo_double(idx) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_int, c_double
USE liblammps
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), VALUE :: idx
REAL(c_double), POINTER :: dval
REAL(c_double) :: f_lammps_last_thermo_double
dval = lmp%last_thermo('data',idx)
f_lammps_last_thermo_double = dval
END FUNCTION f_lammps_last_thermo_double

41
unittest/fortran/wrap_get_thermo.cpp
View File

@ -1,6 +1,7 @@
// unit tests for getting thermodynamic output from a LAMMPS instance through the Fortran wrapper
#include "lammps.h"
#include "lmptype.h"
#include <mpi.h>
#include <string>
@ -23,8 +24,18 @@ double f_lammps_get_thermo_ylo();
double f_lammps_get_thermo_yhi();
double f_lammps_get_thermo_zlo();
double f_lammps_get_thermo_zhi();
void f_lammps_last_thermo_setup();
int f_lammps_last_thermo_step();
int f_lammps_last_thermo_num();
int f_lammps_last_thermo_type(int);
const char *f_lammps_last_thermo_string(int);
int f_lammps_last_thermo_int(int);
double f_lammps_last_thermo_double(int);
}
using LAMMPS_NS::multitype;
class LAMMPS_thermo : public ::testing::Test {
protected:
LAMMPS_NS::LAMMPS *lmp;
@ -65,3 +76,33 @@ TEST_F(LAMMPS_thermo, get_thermo)
EXPECT_DOUBLE_EQ(f_lammps_get_thermo_zlo(), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_get_thermo_zhi(), 4.0);
};
TEST_F(LAMMPS_thermo, last_thermo)
{
EXPECT_EQ(f_lammps_last_thermo_step(), -1);
EXPECT_EQ(f_lammps_last_thermo_type(1), multitype::LAMMPS_NONE);
EXPECT_EQ(f_lammps_last_thermo_type(2), multitype::LAMMPS_NONE);
f_lammps_last_thermo_setup();
EXPECT_EQ(f_lammps_last_thermo_step(), 15);
EXPECT_EQ(f_lammps_last_thermo_num(), 6);
EXPECT_STREQ(f_lammps_last_thermo_string(1), "Step");
EXPECT_STREQ(f_lammps_last_thermo_string(2), "Temp");
EXPECT_STREQ(f_lammps_last_thermo_string(3), "E_pair");
EXPECT_STREQ(f_lammps_last_thermo_string(6), "Press");
#if defined(LAMMPS_SMALLSMALL)
EXPECT_EQ(f_lammps_last_thermo_type(1), multitype::LAMMPS_INT);
#else
EXPECT_EQ(f_lammps_last_thermo_type(1), multitype::LAMMPS_INT64);
#endif
EXPECT_EQ(f_lammps_last_thermo_int(1), 15);
EXPECT_EQ(f_lammps_last_thermo_type(2), multitype::LAMMPS_DOUBLE);
EXPECT_EQ(f_lammps_last_thermo_type(3), multitype::LAMMPS_DOUBLE);
EXPECT_EQ(f_lammps_last_thermo_type(4), multitype::LAMMPS_DOUBLE);
EXPECT_EQ(f_lammps_last_thermo_type(5), multitype::LAMMPS_DOUBLE);
EXPECT_EQ(f_lammps_last_thermo_type(6), multitype::LAMMPS_DOUBLE);
EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(2), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(3), -0.13713425198078993);
EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(4), 0.0);
EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(5), -0.13713425198078993);
EXPECT_DOUBLE_EQ(f_lammps_last_thermo_double(6), -0.022421073321023492);
};

16
unittest/utils/test_lmptype.cpp
View File

@ -54,18 +54,18 @@ TEST(Types, multitype)
m[4] = -1023;
m[5] = -2.225;
EXPECT_EQ(m[0].type, multitype::BIGINT);
EXPECT_EQ(m[1].type, multitype::INT);
EXPECT_EQ(m[2].type, multitype::DOUBLE);
EXPECT_EQ(m[0].type, multitype::LAMMPS_INT64);
EXPECT_EQ(m[1].type, multitype::LAMMPS_INT);
EXPECT_EQ(m[2].type, multitype::LAMMPS_DOUBLE);
#if defined(LAMMPS_SMALLSMALL)
EXPECT_EQ(m[3].type, multitype::INT);
EXPECT_EQ(m[3].type, multitype::LAMMPS_INT);
#else
EXPECT_EQ(m[3].type, multitype::BIGINT);
EXPECT_EQ(m[3].type, multitype::LAMMPS_INT64);
#endif
EXPECT_EQ(m[4].type, multitype::INT);
EXPECT_EQ(m[5].type, multitype::DOUBLE);
EXPECT_EQ(m[6].type, multitype::NONE);
EXPECT_EQ(m[4].type, multitype::LAMMPS_INT);
EXPECT_EQ(m[5].type, multitype::LAMMPS_DOUBLE);
EXPECT_EQ(m[6].type, multitype::LAMMPS_NONE);
EXPECT_EQ(m[0].data.b, b1);
EXPECT_EQ(m[1].data.i, i1);