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Merge branch 'master' into collected-small-changes

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This commit is contained in:
Axel Kohlmeyer
2021-03-03 21:49:48 -05:00
parent 73c874a042 0f63f07ce5
commit 97d1964383
13 changed files with 39 additions and 11 deletions
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2
doc/src/compute_fep.rst
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@ -163,7 +163,7 @@ the meaning of these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+

4
doc/src/fix_adapt.rst
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@ -128,9 +128,9 @@ formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`born/coul/long, born/coul/msm <pair_born>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
| :doc:`buck, buck/coul/cut <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | coulombic_cutoff | type global |
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | a,c,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+

2
doc/src/fix_adapt_fep.rst
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@ -120,7 +120,7 @@ styles and their energy formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+

3
src/KSPACE/pair_buck_coul_long.cpp
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@ -558,5 +558,8 @@ void *PairBuckCoulLong::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
dim = 2;
if (strcmp(str,"a") == 0) return (void *) a;
if (strcmp(str,"c") == 0) return (void *) c;
return nullptr;
}

4
src/KSPACE/pair_buck_coul_msm.cpp
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@ -246,5 +246,9 @@ void *PairBuckCoulMSM::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
dim = 2;
if (strcmp(str,"a") == 0) return (void *) a;
if (strcmp(str,"c") == 0) return (void *) c;
return nullptr;
}

4
src/fix_nh.cpp
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@ -1754,13 +1754,13 @@ void *FixNH::extract(const char *str, int &dim)
} else if (tstat_flag && strcmp(str,"mtchain") == 0) {
return &mtchain;
} else if (pstat_flag && strcmp(str,"mpchain") == 0) {
return &mtchain;
return &mpchain;
}
dim=1;
if (tstat_flag && strcmp(str,"eta") == 0) {
return &eta;
} else if (pstat_flag && strcmp(str,"etap") == 0) {
return &eta;
return &etap;
} else if (pstat_flag && strcmp(str,"p_flag") == 0) {
return &p_flag;
} else if (pstat_flag && strcmp(str,"p_start") == 0) {

10
src/pair_buck_coul_cut.cpp
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@ -470,3 +470,13 @@ double PairBuckCoulCut::single(int i, int j, int itype, int jtype,
}
return eng;
}
/* ---------------------------------------------------------------------- */
void *PairBuckCoulCut::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"a") == 0) return (void *) a;
if (strcmp(str,"c") == 0) return (void *) c;
return nullptr;
}

1
src/pair_buck_coul_cut.h
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@ -40,6 +40,7 @@ class PairBuckCoulCut : public Pair {
void write_data(FILE *);
void write_data_all(FILE *);
virtual double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);
protected:
double cut_lj_global,cut_coul_global;

4
unittest/force-styles/tests/mol-pair-buck_coul_cut.yaml
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@ -25,7 +25,9 @@ pair_coeff: ! |
4 4 127198.698386798 0.207005479340455 37.2289658745028
4 5 127198.698386798 0.207005479340455 37.2289658745028
5 5 127198.698386798 0.207005479340455 37.2289658745028
extract: ! ""
extract: |
a 2
c 2
natoms: 29
init_vdwl: 143.749538808172
init_coul: -127.494586297384

4
unittest/force-styles/tests/mol-pair-buck_coul_long.yaml
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@ -30,7 +30,9 @@ pair_coeff: ! |
4 4 127198.698386798 0.207005479340455 37.2289658745028
4 5 127198.698386798 0.207005479340455 37.2289658745028
5 5 127198.698386798 0.207005479340455 37.2289658745028
extract: ! ""
extract: |
a 2
c 2
natoms: 29
init_vdwl: 143.749538808172
init_coul: 225.821815126925

4
unittest/force-styles/tests/mol-pair-buck_coul_msm.yaml
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@ -32,7 +32,9 @@ pair_coeff: ! |
4 4 127198.698386798 0.207005479340455 37.2289658745028
4 5 127198.698386798 0.207005479340455 37.2289658745028
5 5 127198.698386798 0.207005479340455 37.2289658745028
extract: ! ""
extract: |
a 2
c 2
natoms: 29
init_vdwl: 143.749538808172
init_coul: 226.465163473713

4
unittest/force-styles/tests/mol-pair-buck_coul_msm_table.yaml
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@ -32,7 +32,9 @@ pair_coeff: ! |
4 4 127198.698386798 0.207005479340455 37.2289658745028
4 5 127198.698386798 0.207005479340455 37.2289658745028
5 5 127198.698386798 0.207005479340455 37.2289658745028
extract: ! ""
extract: |
a 2
c 2
natoms: 29
init_vdwl: 143.749538808172
init_coul: 226.465163473713

4
unittest/force-styles/tests/mol-pair-buck_coul_table.yaml
View File

@ -30,7 +30,9 @@ pair_coeff: ! |
4 4 127198.698386798 0.207005479340455 37.2289658745028
4 5 127198.698386798 0.207005479340455 37.2289658745028
5 5 127198.698386798 0.207005479340455 37.2289658745028
extract: ! ""
extract: |
a 2
c 2
natoms: 29
init_vdwl: 143.749538808172
init_coul: 225.821851347828