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Merge branch 'develop' into cmake-cpp-std-deprecation

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This commit is contained in:
Axel Kohlmeyer
2024-10-15 17:40:59 -04:00
parent 74e449605a 59bbc5bcc1
commit d5c5e164e1
26 changed files with 181 additions and 34 deletions
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64
doc/src/fix_adapt.rst
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@ -323,7 +323,7 @@ If :doc:`bond_style hybrid <bond_hybrid>` is used, *bstyle* should be a
sub-style name. The bond styles that currently work with fix adapt are:
+-----------------------------------------------------+---------------------------+------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
| :doc:`class2 <bond_class2>` | k2,k3,k4,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
@ -331,6 +331,8 @@ sub-style name. The bond styles that currently work with fix adapt are:
+-----------------------------------------------------+---------------------------+------------+
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`gaussian <bond_gaussian>` | alpha,width,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
@ -343,9 +345,9 @@ sub-style name. The bond styles that currently work with fix adapt are:
+-----------------------------------------------------+---------------------------+------------+
| :doc:`mm3 <bond_mm3>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
| :doc:`morse <bond_morse>` | d0,alpha,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
| :doc:`nonlinear <bond_nonlinear>` | lamda,epsilon,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
----------
@ -369,31 +371,37 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
If :doc:`angle_style hybrid <angle_hybrid>` is used, *astyle* should be a
sub-style name. The angle styles that currently work with fix adapt are:
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`charmm <angle_charmm>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`class2 <angle_class2>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine/periodic <angle_cosine_periodic>` | k,b,n | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`dipole <angle_dipole>` | k,gamma0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`fourier <angle_fourier>` | k,c0,c1,c2 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`fourier/simple <angle_fourier_simple>` | k,c,n | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`mm3 <angle_mm3>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`quartic <angle_quartic>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`spica <angle_spica>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`charmm <angle_charmm>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`class2 <angle_class2>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine/delta <angle_cosine_delta>` | k | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine/periodic <angle_cosine_periodic>` | k,b,n | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine/squared <angle_cosine_squared>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`dipole <angle_dipole>` | k,gamma0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`fourier <angle_fourier>` | k,c0,c1,c2 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`fourier/simple <angle_fourier_simple>` | k,c,n | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`gaussian <angle_gaussian>` | alpha,width,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`mm3 <angle_mm3>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`quartic <angle_quartic>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`spica <angle_spica>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
Note that internally, theta0 is stored in radians, so the variable
this fix uses to reset theta0 needs to generate values in radians.

16
src/AMOEBA/angle_amoeba.cpp
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@ -868,3 +868,19 @@ double AngleAmoeba::single(int type, int i1, int i2, int i3)
return energy;
}
/* ----------------------------------------------------------------------
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *AngleAmoeba::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "k2") == 0) return (void *) k2;
if (strcmp(str, "k3") == 0) return (void *) k3;
if (strcmp(str, "k4") == 0) return (void *) k4;
if (strcmp(str, "k5") == 0) return (void *) k5;
if (strcmp(str, "k6") == 0) return (void *) k6;
if (strcmp(str, "theta0") == 0) return (void *) theta0;
return nullptr;
}

1
src/AMOEBA/angle_amoeba.h
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@ -36,6 +36,7 @@ class AngleAmoeba : public Angle {
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, int, int, int) override;
void *extract(const char *, int &) override;
protected:
int *pflag, *ubflag;

3
src/CLASS2/bond_class2.cpp
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@ -242,6 +242,9 @@ void BondClass2::born_matrix(int type, double rsq, int /*i*/, int /*j*/, double
void *BondClass2::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "k2") == 0) return (void *) k2;
if (strcmp(str, "k3") == 0) return (void *) k3;
if (strcmp(str, "k4") == 0) return (void *) k4;
if (strcmp(str,"r0")==0) return (void*) r0;
return nullptr;
}

11
src/EXTRA-MOLECULE/angle_gaussian.cpp
View File

@ -352,3 +352,14 @@ double AngleGaussian::single(int type, int i1, int i2, int i3)
if (sum_g_i < SMALL) sum_g_i = SMALL;
return -(force->boltz * angle_temperature[type]) * log(sum_g_i);
}
/* ---------------------------------------------------------------------- */
void *AngleGaussian::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"alpha") == 0) return (void *) alpha;
if (strcmp(str,"width") == 0) return (void *) width;
if (strcmp(str,"theta0") == 0) return (void *) theta0;
return nullptr;
}

1
src/EXTRA-MOLECULE/angle_gaussian.h
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@ -35,6 +35,7 @@ class AngleGaussian : public Angle {
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, int, int, int) override;
void *extract(const char *, int &) override;
protected:
int *nterms;

11
src/EXTRA-MOLECULE/bond_gaussian.cpp
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@ -337,3 +337,14 @@ void BondGaussian::born_matrix(int type, double rsq, int /*i*/, int /*j*/, doubl
du2 = - (force->boltz * bond_temperature[type]) * numerator / denominator;
}
/* ---------------------------------------------------------------------- */
void *BondGaussian::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"alpha") == 0) return (void *) alpha;
if (strcmp(str,"width") == 0) return (void *) width;
if (strcmp(str,"r0") == 0) return (void *) r0;
return nullptr;
}

1
src/EXTRA-MOLECULE/bond_gaussian.h
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@ -36,6 +36,7 @@ class BondGaussian : public Bond {
void write_data(FILE *) override;
double single(int, double, int, int, double &) override;
void born_matrix(int, double, int, int, double &, double &) override;
void *extract(const char *, int &) override;
protected:
int *nterms;

1
src/EXTRA-MOLECULE/bond_nonlinear.cpp
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@ -228,6 +228,7 @@ void BondNonlinear::born_matrix(int type, double rsq, int /*i*/, int /*j*/, doub
void *BondNonlinear::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str,"lamda")==0) return (void*) lamda;
if (strcmp(str,"epsilon")==0) return (void*) epsilon;
if (strcmp(str,"r0")==0) return (void*) r0;
return nullptr;

11
src/MESONT/angle_mesocnt.cpp
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@ -396,3 +396,14 @@ double AngleMesoCNT::single(int type, int i1, int i2, int i3)
else
return kb[type] * dtheta + thetab[type] * (kh[type] * thetab[type] - kb[type]);
}
/* ----------------------------------------------------------------------
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *AngleMesoCNT::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "theta0") == 0) return (void *) theta0;
return nullptr;
}

1
src/MESONT/angle_mesocnt.h
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@ -41,6 +41,7 @@ class AngleMesoCNT : public Angle {
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, int, int, int) override;
void *extract(const char *, int &) override;
protected:
int *buckling;

16
src/MOFFF/angle_class2_p6.cpp
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@ -487,3 +487,19 @@ double AngleClass2P6::single(int type, int i1, int i2, int i3)
return energy;
}
/* ----------------------------------------------------------------------
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *AngleClass2P6::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "k2") == 0) return (void *) k2;
if (strcmp(str, "k3") == 0) return (void *) k3;
if (strcmp(str, "k4") == 0) return (void *) k4;
if (strcmp(str, "k5") == 0) return (void *) k5;
if (strcmp(str, "k6") == 0) return (void *) k6;
if (strcmp(str, "theta0") == 0) return (void *) theta0;
return nullptr;
}

1
src/MOFFF/angle_class2_p6.h
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@ -35,6 +35,7 @@ class AngleClass2P6 : public Angle {
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, int, int, int) override;
void *extract(const char *, int &) override;
protected:
double *theta0, *k2, *k3, *k4, *k5, *k6;

13
src/MOFFF/angle_cosine_buck6d.cpp
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@ -383,3 +383,16 @@ double AngleCosineBuck6d::single(int type, int i1, int i2, int i3)
return k[type]*(1.0+cos(tk));
}
/* ----------------------------------------------------------------------
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *AngleCosineBuck6d::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "k") == 0) return (void *) k;
if (strcmp(str, "multiplicity") == 0) return (void *) multiplicity;
if (strcmp(str, "th0") == 0) return (void *) th0;
return nullptr;
}

1
src/MOFFF/angle_cosine_buck6d.h
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@ -36,6 +36,7 @@ class AngleCosineBuck6d : public Angle {
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, int, int, int) override;
void *extract(const char *, int &) override;
protected:
double *k, *th0;

2
src/MOLECULE/bond_morse.cpp
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@ -227,6 +227,8 @@ void BondMorse::born_matrix(int type, double rsq, int /*i*/, int /*j*/, double &
void *BondMorse::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "d0") == 0) return (void *) d0;
if (strcmp(str, "alpha") == 0) return (void *) alpha;
if (strcmp(str, "r0") == 0) return (void *) r0;
return nullptr;
}

16
src/YAFF/angle_cross.cpp
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@ -342,3 +342,19 @@ double AngleCross::single(int type, int i1, int i2, int i3)
double energy = kss[type]*dr1*dr2+kbs0[type]*dr1*dtheta + kbs1[type]*dr2*dtheta;
return energy;
}
/* ----------------------------------------------------------------------
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *AngleCross::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "r00") == 0) return (void *) r00;
if (strcmp(str, "r01") == 0) return (void *) r01;
if (strcmp(str, "kss") == 0) return (void *) kss;
if (strcmp(str, "kbs0") == 0) return (void *) kbs0;
if (strcmp(str, "kbs1") == 0) return (void *) kbs1;
if (strcmp(str, "theta0") == 0) return (void *) theta0;
return nullptr;
}

1
src/YAFF/angle_cross.h
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@ -35,6 +35,7 @@ class AngleCross : public Angle {
void read_restart(FILE *) override;
void write_data(FILE *) override;
double single(int, int, int, int) override;
void *extract(const char *, int &) override;
protected:
double *kss, *kbs0, *kbs1, *r00, *r01, *theta0;

8
unittest/force-styles/tests/angle-amoeba.yaml
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@ -20,7 +20,13 @@ angle_coeff: ! |
* ub 0.0 0.0
4 ub -7.6 1.5537
equilibrium: 4 1.9320794819577227 1.9687313962496038 2.1676989309769574 1.8936822384138474
extract: ! ""
extract: ! |
k2 1
k3 1
k4 1
k5 1
k6 1
theta0 1
natoms: 29
init_energy: 22.644137017730763
init_stress: ! |2-

8
unittest/force-styles/tests/angle-class2_p6.yaml
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@ -23,7 +23,13 @@ angle_coeff: ! |
3 ba 10.0 10.0 1.5 1.5
4 ba 0.0 20.0 1.5 1.5
equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
extract: ! ""
extract: ! |
k2 1
k3 1
k4 1
k5 1
k6 1
theta0 1
natoms: 29
init_energy: 46.44080287964778
init_stress: ! |2-

8
unittest/force-styles/tests/angle-cross.yaml
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@ -16,7 +16,13 @@ angle_coeff: ! |
3 100.0 150.0 120.0 1.45 1.35 98.2
4 250.0 90.0 110.0 1.05 1.20 99.9
equilibrium: 4 1.8675022996339325 1.911135530933791 1.7139133254584316 1.7435839227423353
extract: ! ""
extract: ! |
r00 1
r01 1
kss 1
kbs0 1
kbs1 1
theta0 1
natoms: 29
init_energy: -138.93227715361755
init_stress: ! |-

5
unittest/force-styles/tests/angle-gaussian.yaml
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@ -16,7 +16,10 @@ angle_coeff: ! |
3 300.0 2 0.2189 8.66 88.1 0.5439 9.94 142.7
4 300.0 2 0.0214 14.29 85.3 0.3934 18.22 118.1
equilibrium: 4 1.5376350710070041 1.4887658519511628 1.5376350710070041 1.4887658519511628
extract: ! ""
extract: ! |
alpha 2
width 2
theta0 2
natoms: 29
init_energy: 57.794009158943744
init_stress: ! |2-

3
unittest/force-styles/tests/bond-class2.yaml
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@ -18,6 +18,9 @@ bond_coeff: ! |
5 0.97 532.50 -1282.90 2004.76
equilibrium: 5 1.42 1.1 1.3 1.2 0.97
extract: ! |
k2 1
k3 1
k4 1
r0 1
natoms: 29
init_energy: 26.429859642132705

5
unittest/force-styles/tests/bond-gaussian.yaml
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@ -17,7 +17,10 @@ bond_coeff: ! |
4 300.0 1 0.0100 0.098 2.45
5 300.0 1 0.0100 0.098 2.85
equilibrium: 5 1.45 1.37 1.61 2.45 2.85
extract: ! ""
extract: ! |
alpha 2
width 2
r0 2
natoms: 29
init_energy: 4638.6541482649545
init_stress: ! |2-

2
unittest/force-styles/tests/bond-morse.yaml
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@ -18,6 +18,8 @@ bond_coeff: ! |
5 7000.0 0.3 1.0
equilibrium: 5 1.5 1.1 1.3 1.2 1
extract: ! |
d0 1
alpha 1
r0 1
natoms: 29
init_energy: 5.607154540709207

5
unittest/force-styles/tests/bond-nonlinear.yaml
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@ -17,7 +17,10 @@ bond_coeff: ! |
4 650.0 1.2 1.4
5 450.0 1.0 1.1
equilibrium: 5 1.5 1.1 1.3 1.2 1
extract: ! ""
extract: ! |
lamda 1
epsilon 1
r0 1
natoms: 29
init_energy: 1.9451728032820943
init_stress: ! |-