Uncrustified code changes since 4.6

The group kernel python scripts have changed slightly to emit
code that uncrustify won't want to change. Group kernel
generation and uncrustify are now mutual null operations.

Recent changes to the declarations in gmx_order in baa65b60
may have exposed a possible bug in uncrustify. Those declarations
have been simplified so that there will be no future issue from
that possible bug.

Refs #845

Change-Id: I33495d57ca37317cef4bf12707fd77d67309d292

diff --git a/src/gmxlib/nonbonded/nb_kernel_adress_c/make_nb_kernel_adress_c.py b/src/gmxlib/nonbonded/nb_kernel_adress_c/make_nb_kernel_adress_c.py
index 8232ba0ea21fbd392d383060dc3e768db38321be..01bc4ef89f2fe0b4e245ab857304306f7614fb7a 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_adress_c/make_nb_kernel_adress_c.py
+++ b/src/gmxlib/nonbonded/nb_kernel_adress_c/make_nb_kernel_adress_c.py
@@ -531,13 +531,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/make_nb_kernel_avx_128_fma_double.py b/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/make_nb_kernel_avx_128_fma_double.py
index 35a8fc3b3383f8edb9aaa018c716ff1edd8af7a9..3b435554ba2ada646c4b290b8dc9ae0c4f781df5 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/make_nb_kernel_avx_128_fma_double.py
+++ b/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/make_nb_kernel_avx_128_fma_double.py
@@ -526,13 +526,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c b/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
index 8f157e3b8f42a7072a6b618fc09a0d7256e4b378..9ab3a5c97181ff9863a3400e4ff86dc132c5dfe1 100644 (file)
--- a/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
+++ b/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
@@ -257,7 +257,7 @@ nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_double;
 
 
 nb_kernel_info_t
-kernellist_avx_128_fma_double[] =
+    kernellist_avx_128_fma_double[] =
 {
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
@@ -476,6 +476,6 @@ kernellist_avx_128_fma_double[] =
 };
 
 int
-kernellist_avx_128_fma_double_size = sizeof(kernellist_avx_128_fma_double)/sizeof(kernellist_avx_128_fma_double[0]);
+    kernellist_avx_128_fma_double_size = sizeof(kernellist_avx_128_fma_double)/sizeof(kernellist_avx_128_fma_double[0]);
 
 #endif

diff --git a/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/make_nb_kernel_avx_128_fma_single.py b/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/make_nb_kernel_avx_128_fma_single.py
index eac82ebf699fd5518f235a48561798d0e74a91c5..cff120d4aff20fa1672ea0ed4fe0fa560aeb03e1 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/make_nb_kernel_avx_128_fma_single.py
+++ b/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/make_nb_kernel_avx_128_fma_single.py
@@ -526,13 +526,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c b/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
index a8b3c2236d18f0e24ec4391524efc7372b6dcd5f..8783ae2a6dcb84c5c576ebb82736566d013cde1a 100644 (file)
--- a/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
+++ b/src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
@@ -257,7 +257,7 @@ nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_single;
 
 
 nb_kernel_info_t
-kernellist_avx_128_fma_single[] =
+    kernellist_avx_128_fma_single[] =
 {
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
@@ -476,6 +476,6 @@ kernellist_avx_128_fma_single[] =
 };
 
 int
-kernellist_avx_128_fma_single_size = sizeof(kernellist_avx_128_fma_single)/sizeof(kernellist_avx_128_fma_single[0]);
+    kernellist_avx_128_fma_single_size = sizeof(kernellist_avx_128_fma_single)/sizeof(kernellist_avx_128_fma_single[0]);
 
 #endif

diff --git a/src/gmxlib/nonbonded/nb_kernel_avx_256_double/make_nb_kernel_avx_256_double.py b/src/gmxlib/nonbonded/nb_kernel_avx_256_double/make_nb_kernel_avx_256_double.py
index 4644e6d247e9b59e2f6dabe7438fdde0b9039ea9..afd6a606c352f199e6bd66deea4749273a061d78 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_avx_256_double/make_nb_kernel_avx_256_double.py
+++ b/src/gmxlib/nonbonded/nb_kernel_avx_256_double/make_nb_kernel_avx_256_double.py
@@ -526,13 +526,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c b/src/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
index f437d6d5a33e18e745d3942ffeef690a8ed7794e..5a9bb4166793e00f847e88036dd95f02a73dec1a 100644 (file)
--- a/src/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
+++ b/src/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
@@ -257,7 +257,7 @@ nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_double;
 
 
 nb_kernel_info_t
-kernellist_avx_256_double[] =
+    kernellist_avx_256_double[] =
 {
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_256_double", "avx_256_double", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_avx_256_double, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_avx_256_double", "avx_256_double", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
@@ -476,6 +476,6 @@ kernellist_avx_256_double[] =
 };
 
 int
-kernellist_avx_256_double_size = sizeof(kernellist_avx_256_double)/sizeof(kernellist_avx_256_double[0]);
+    kernellist_avx_256_double_size = sizeof(kernellist_avx_256_double)/sizeof(kernellist_avx_256_double[0]);
 
 #endif

diff --git a/src/gmxlib/nonbonded/nb_kernel_avx_256_single/make_nb_kernel_avx_256_single.py b/src/gmxlib/nonbonded/nb_kernel_avx_256_single/make_nb_kernel_avx_256_single.py
index dc27ca638c0ca60e2aca6ddde113b8e2cc362606..b2cf2e961b286df4c281bbb05d6cf4a2cce0785d 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_avx_256_single/make_nb_kernel_avx_256_single.py
+++ b/src/gmxlib/nonbonded/nb_kernel_avx_256_single/make_nb_kernel_avx_256_single.py
@@ -526,13 +526,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c b/src/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
index 1f683b5198cd9e66a2fbd7a9039b8a06b61a4a29..73a21850b634daacc5880d111df733255f98dec5 100644 (file)
--- a/src/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
+++ b/src/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
@@ -257,7 +257,7 @@ nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_single;
 
 
 nb_kernel_info_t
-kernellist_avx_256_single[] =
+    kernellist_avx_256_single[] =
 {
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_avx_256_single", "avx_256_single", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_avx_256_single, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_avx_256_single", "avx_256_single", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
@@ -476,6 +476,6 @@ kernellist_avx_256_single[] =
 };
 
 int
-kernellist_avx_256_single_size = sizeof(kernellist_avx_256_single)/sizeof(kernellist_avx_256_single[0]);
+    kernellist_avx_256_single_size = sizeof(kernellist_avx_256_single)/sizeof(kernellist_avx_256_single[0]);
 
 #endif

diff --git a/src/gmxlib/nonbonded/nb_kernel_c/make_nb_kernel_c.py b/src/gmxlib/nonbonded/nb_kernel_c/make_nb_kernel_c.py
index 3c93ddd4269b5f231cbf08aeea69bd2aeb326412..44f22ceeebea6e0e85267fbc2a8b78f4c3945570 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_c/make_nb_kernel_c.py
+++ b/src/gmxlib/nonbonded/nb_kernel_c/make_nb_kernel_c.py
@@ -526,13 +526,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c b/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
index 12ab8fc8991d57ba61770d1856e544a67f14b9ff..3d6ff12132649bf1e94b942d391b16b83564fffb 100644 (file)
--- a/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
+++ b/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
@@ -345,7 +345,7 @@ nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c;
 
 
 nb_kernel_info_t
-kernellist_c[] =
+    kernellist_c[] =
 {
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_c", "c", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_c", "c", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
@@ -652,6 +652,6 @@ kernellist_c[] =
 };
 
 int
-kernellist_c_size = sizeof(kernellist_c)/sizeof(kernellist_c[0]);
+    kernellist_c_size = sizeof(kernellist_c)/sizeof(kernellist_c[0]);
 
 #endif

diff --git a/src/gmxlib/nonbonded/nb_kernel_sse2_double/make_nb_kernel_sse2_double.py b/src/gmxlib/nonbonded/nb_kernel_sse2_double/make_nb_kernel_sse2_double.py
index 352faab684499bbae9c277c9396b06510ef51267..59f4e59168678da38b6b8ffaf815a29655d60405 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_sse2_double/make_nb_kernel_sse2_double.py
+++ b/src/gmxlib/nonbonded/nb_kernel_sse2_double/make_nb_kernel_sse2_double.py
@@ -526,13 +526,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c b/src/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
index 2bd1c3b2fa30cc4619ff34273da3e830abd19524..ca55fb6e3a537eb36c15834d37e5e061fee788a8 100644 (file)
--- a/src/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
+++ b/src/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
@@ -257,7 +257,7 @@ nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_double;
 
 
 nb_kernel_info_t
-kernellist_sse2_double[] =
+    kernellist_sse2_double[] =
 {
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_sse2_double, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_sse2_double", "sse2_double", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_sse2_double, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_sse2_double", "sse2_double", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
@@ -476,6 +476,6 @@ kernellist_sse2_double[] =
 };
 
 int
-kernellist_sse2_double_size = sizeof(kernellist_sse2_double)/sizeof(kernellist_sse2_double[0]);
+    kernellist_sse2_double_size = sizeof(kernellist_sse2_double)/sizeof(kernellist_sse2_double[0]);
 
 #endif

diff --git a/src/gmxlib/nonbonded/nb_kernel_sse2_single/make_nb_kernel_sse2_single.py b/src/gmxlib/nonbonded/nb_kernel_sse2_single/make_nb_kernel_sse2_single.py
index ad43b3ba6e9fe21295153592ad864d38d02aaf93..4cf6e5f68800979ba16cedf4d90409b676be4280 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_sse2_single/make_nb_kernel_sse2_single.py
+++ b/src/gmxlib/nonbonded/nb_kernel_sse2_single/make_nb_kernel_sse2_single.py
@@ -526,13 +526,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c b/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
index 6002013d2452b32e61fe0a83e9a773d59179bc5f..fb46f4b3ba505789671a55a1134ed766be27a2ca 100644 (file)
--- a/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
+++ b/src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
@@ -257,7 +257,7 @@ nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_single;
 
 
 nb_kernel_info_t
-kernellist_sse2_single[] =
+    kernellist_sse2_single[] =
 {
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_sse2_single, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_sse2_single", "sse2_single", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_sse2_single, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_sse2_single", "sse2_single", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
@@ -476,6 +476,6 @@ kernellist_sse2_single[] =
 };
 
 int
-kernellist_sse2_single_size = sizeof(kernellist_sse2_single)/sizeof(kernellist_sse2_single[0]);
+    kernellist_sse2_single_size = sizeof(kernellist_sse2_single)/sizeof(kernellist_sse2_single[0]);
 
 #endif

diff --git a/src/gmxlib/nonbonded/nb_kernel_sse4_1_double/make_nb_kernel_sse4_1_double.py b/src/gmxlib/nonbonded/nb_kernel_sse4_1_double/make_nb_kernel_sse4_1_double.py
index a34738ae2811c6a57077fb0461f7dc2e1e9353f5..476b303990f75fe16f18441222672fa9dfe0855d 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_sse4_1_double/make_nb_kernel_sse4_1_double.py
+++ b/src/gmxlib/nonbonded/nb_kernel_sse4_1_double/make_nb_kernel_sse4_1_double.py
@@ -526,13 +526,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c b/src/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
index 665c685bee0faa8d6444e4c5b4919038bd13d028..1661f658754278731a3089a67506b322a6b515f2 100644 (file)
--- a/src/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
+++ b/src/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
@@ -257,7 +257,7 @@ nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_double;
 
 
 nb_kernel_info_t
-kernellist_sse4_1_double[] =
+    kernellist_sse4_1_double[] =
 {
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_sse4_1_double", "sse4_1_double", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
@@ -476,6 +476,6 @@ kernellist_sse4_1_double[] =
 };
 
 int
-kernellist_sse4_1_double_size = sizeof(kernellist_sse4_1_double)/sizeof(kernellist_sse4_1_double[0]);
+    kernellist_sse4_1_double_size = sizeof(kernellist_sse4_1_double)/sizeof(kernellist_sse4_1_double[0]);
 
 #endif

diff --git a/src/gmxlib/nonbonded/nb_kernel_sse4_1_single/make_nb_kernel_sse4_1_single.py b/src/gmxlib/nonbonded/nb_kernel_sse4_1_single/make_nb_kernel_sse4_1_single.py
index f13947d29881436f8d36a305ead2bda147503d31..3dfb46aa6850bbcb6a288c1747cedc18ea4e4553 100755 (executable)
--- a/src/gmxlib/nonbonded/nb_kernel_sse4_1_single/make_nb_kernel_sse4_1_single.py
+++ b/src/gmxlib/nonbonded/nb_kernel_sse4_1_single/make_nb_kernel_sse4_1_single.py
@@ -526,13 +526,13 @@ pass
 # Write out the list of settings and corresponding kernels to the declaration file
 fpdecl.write( '\n\n' )
 fpdecl.write( 'nb_kernel_info_t\n' )
-fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '    kernellist_'+Arch+'[] =\n' )
 fpdecl.write( '{\n' )
 for decl in kerneldecl[0:-1]:
     fpdecl.write( decl + ',\n' )
 fpdecl.write( kerneldecl[-1] + '\n' )
 fpdecl.write( '};\n\n' )
 fpdecl.write( 'int\n' )
-fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '    kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
 fpdecl.write( '#endif\n')
 fpdecl.close()

diff --git a/src/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c b/src/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
index f774874ff1187c2b2b3fd6f875e0a5d3f88ae923..cf1d322c1d8341030ada8ff2aa3ab8767fdba303 100644 (file)
--- a/src/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
+++ b/src/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
@@ -257,7 +257,7 @@ nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_single;
 
 
 nb_kernel_info_t
-kernellist_sse4_1_single[] =
+    kernellist_sse4_1_single[] =
 {
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
     { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_sse4_1_single", "sse4_1_single", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
@@ -476,6 +476,6 @@ kernellist_sse4_1_single[] =
 };
 
 int
-kernellist_sse4_1_single_size = sizeof(kernellist_sse4_1_single)/sizeof(kernellist_sse4_1_single[0]);
+    kernellist_sse4_1_single_size = sizeof(kernellist_sse4_1_single)/sizeof(kernellist_sse4_1_single[0]);
 
 #endif

diff --git a/src/gmxlib/thread_mpi/pthreads.c b/src/gmxlib/thread_mpi/pthreads.c
index d49dc1245c0f75122539971ce0873d9f2bde6da3..948ae78aa72b3de39b3c18ad28579e89323df6b3 100644 (file)
--- a/src/gmxlib/thread_mpi/pthreads.c
+++ b/src/gmxlib/thread_mpi/pthreads.c
@@ -274,10 +274,10 @@ enum tMPI_Thread_setaffinity_support tMPI_Thread_setaffinity_support(void)
 {
 #ifdef HAVE_PTHREAD_SETAFFINITY
     cpu_set_t set;
-    int ret;
+    int       ret;
 
     /* run getaffinity to check whether we get back ENOSYS */
-    ret=pthread_getaffinity_np(pthread_self(), sizeof(set), &set);
+    ret = pthread_getaffinity_np(pthread_self(), sizeof(set), &set);
     if (ret == 0)
     {
         return TMPI_SETAFFINITY_SUPPORT_YES;

diff --git a/src/mdlib/forcerec.c b/src/mdlib/forcerec.c
index 24e467017e120d4b104e9a95fa3ccab938c3adb2..2253eb105106bf3568d65dbccd8c4c9ea7a14cb8 100644 (file)
--- a/src/mdlib/forcerec.c
+++ b/src/mdlib/forcerec.c
@@ -1392,9 +1392,9 @@ static void make_adress_tf_tables(FILE *fp, const output_env_t oenv,
         j = ir->adress->tf_table_index[i]; /* get energy group index */
         sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "tf_%s.%s",
                 *(mtop->groups.grpname[mtop->groups.grps[egcENER].nm_ind[j]]), ftp2ext(efXVG));
-        if(fp)
+        if (fp)
         {
-           fprintf(fp,"loading tf table for energygrp index %d from %s\n", ir->adress->tf_table_index[i], buf);
+            fprintf(fp, "loading tf table for energygrp index %d from %s\n", ir->adress->tf_table_index[i], buf);
         }
         fr->atf_tabs[i] = make_atf_table(fp, oenv, fr, buf, box);
     }

diff --git a/src/mdlib/nbnxn_atomdata.c b/src/mdlib/nbnxn_atomdata.c
index 6e70d98cdd5cbfe920040f592407a7b866105d7b..1ad0502599b700eff0cfd0822f7b64a4e4e80707 100644 (file)
--- a/src/mdlib/nbnxn_atomdata.c
+++ b/src/mdlib/nbnxn_atomdata.c
@@ -1221,8 +1221,8 @@ nbnxn_atomdata_add_nbat_f_to_f_part(const nbnxn_search_t nbs,
                 }
             }
             break;
-    default:
-        gmx_incons("Unsupported nbnxn_atomdata_t format");
+        default:
+            gmx_incons("Unsupported nbnxn_atomdata_t format");
     }
 }
 

diff --git a/src/mdlib/nbnxn_internal.h b/src/mdlib/nbnxn_internal.h
index 558d8b25a5ce369d32365549feec894aa7dc41e9..b0eaf2e459aa96b9514415cc461e1259f12c8474 100644 (file)
--- a/src/mdlib/nbnxn_internal.h
+++ b/src/mdlib/nbnxn_internal.h
@@ -143,16 +143,16 @@ typedef struct nbnxn_list_work {
     nbnxn_x_ci_simd_4xn_t  *x_ci_simd_4xn;
     nbnxn_x_ci_simd_2xnn_t *x_ci_simd_2xnn;
 #endif
-    int                     cj_ind;    /* The current cj_ind index for the current list     */
-    int                     cj4_init;  /* The first unitialized cj4 block                   */
+    int                     cj_ind;          /* The current cj_ind index for the current list     */
+    int                     cj4_init;        /* The first unitialized cj4 block                   */
 
-    float                  *d2;        /* Bounding box distance work array                  */
+    float                  *d2;              /* Bounding box distance work array                  */
 
-    nbnxn_cj_t             *cj;        /* The j-cell list                                   */
-    int                     cj_nalloc; /* Allocation size of cj                             */
+    nbnxn_cj_t             *cj;              /* The j-cell list                                   */
+    int                     cj_nalloc;       /* Allocation size of cj                             */
 
-    int                     ncj_noq;   /* Nr. of cluster pairs without Coul for flop count  */
-    int                     ncj_hlj;   /* Nr. of cluster pairs with 1/2 LJ for flop count   */
+    int                     ncj_noq;         /* Nr. of cluster pairs without Coul for flop count  */
+    int                     ncj_hlj;         /* Nr. of cluster pairs with 1/2 LJ for flop count   */
 
     int                    *sort;            /* Sort index                    */
     int                     sort_nalloc;     /* Allocation size of sort       */
@@ -160,7 +160,7 @@ typedef struct nbnxn_list_work {
     nbnxn_sci_t            *sci_sort;        /* Second sci array, for sorting */
     int                     sci_sort_nalloc; /* Allocation size of sci_sort   */
 
-    gmx_cache_protect_t     cp1;       /* Protect cache between threads               */
+    gmx_cache_protect_t     cp1;             /* Protect cache between threads               */
 } nbnxn_list_work_t;
 
 /* Function type for setting the i-atom coordinate working data */

diff --git a/src/mdlib/nbnxn_search.c b/src/mdlib/nbnxn_search.c
index 6e0ea13d9197c40ec6f24c2cf93195c6b8a5f0c5..c16d4aa9dc470ef816a917f51d87341fa9e76740 100644 (file)
--- a/src/mdlib/nbnxn_search.c
+++ b/src/mdlib/nbnxn_search.c
@@ -2957,11 +2957,11 @@ static void make_cluster_list_supersub(const nbnxn_search_t nbs,
             if (d2 < rbb2 ||
                 (d2 < rl2 &&
 #ifdef NBNXN_PBB_SSE
-                subc_in_range_sse8
+                 subc_in_range_sse8
 #else
-                subc_in_range_x
+                 subc_in_range_x
 #endif
-                    (na_c, ci, x_ci, cj_gl, stride, x, rl2)))
+                     (na_c, ci, x_ci, cj_gl, stride, x, rl2)))
 #else
             /* Check if the distance between the two bounding boxes
              * in within the pair-list cut-off.
@@ -3904,7 +3904,7 @@ static void print_nblist_sci_cj(FILE *fp, const nbnxn_pairlist_t *nbl)
                 fprintf(fp, "  sj %5d  imask %x\n",
                         nbl->cj4[j4].cj[j],
                         nbl->cj4[j4].imei[0].imask);
-                for (si=0; si<GPU_NSUBCELL; si++)
+                for (si = 0; si < GPU_NSUBCELL; si++)
                 {
                     if (nbl->cj4[j4].imei[0].imask & (1U << (j*GPU_NSUBCELL + si)))
                     {
@@ -4831,19 +4831,19 @@ static void sort_sci(nbnxn_pairlist_t *nbl)
     }
 
     /* Count the entries of each size */
-    for(i = 0; i <= m; i++)
+    for (i = 0; i <= m; i++)
     {
         work->sort[i] = 0;
     }
-    for(s = 0; s < nbl->nsci; s++)
+    for (s = 0; s < nbl->nsci; s++)
     {
         i = min(m, nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start);
         work->sort[i]++;
     }
     /* Calculate the offset for each count */
-    s0           = work->sort[m];
+    s0            = work->sort[m];
     work->sort[m] = 0;
-    for(i = m - 1; i >= 0; i--)
+    for (i = m - 1; i >= 0; i--)
     {
         s1            = work->sort[i];
         work->sort[i] = work->sort[i + 1] + s0;
@@ -4852,7 +4852,7 @@ static void sort_sci(nbnxn_pairlist_t *nbl)
 
     /* Sort entries directly into place */
     sci_sort = work->sci_sort;
-    for(s = 0; s < nbl->nsci; s++)
+    for (s = 0; s < nbl->nsci; s++)
     {
         i = min(m, nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start);
         sci_sort[work->sort[i]++] = nbl->sci[s];

diff --git a/src/mdlib/ns.c b/src/mdlib/ns.c
index 85dbe597aba8fd9c536a54eb5f427e12311a804e..1f137b363efcf545f149a9c5995328a498b38b53 100644 (file)
--- a/src/mdlib/ns.c
+++ b/src/mdlib/ns.c
@@ -1282,14 +1282,14 @@ put_in_list_adress(gmx_bool              bHaveVdW[],
                      * processed by the generic AdResS kernel.
                      */
                     if ( (bEnergyGroupCG &&
-                         wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS ) ||
-                           ( !bEnergyGroupCG && wf[jj] <= GMX_REAL_EPS ) )
+                          wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS ) ||
+                         ( !bEnergyGroupCG && wf[jj] <= GMX_REAL_EPS ) )
                     {
                         continue;
                     }
 
                     b_hybrid = !((wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS) ||
-                        (wf[i_atom] <= GMX_REAL_EPS && wf[jj] <= GMX_REAL_EPS));
+                                 (wf[i_atom] <= GMX_REAL_EPS && wf[jj] <= GMX_REAL_EPS));
 
                     if (bNotEx)
                     {

diff --git a/src/tools/gmx_dipoles.c b/src/tools/gmx_dipoles.c
index fe436dff021bfd494a485f60d71c7f5372e34159..0781d95a14376a2b94118816b1897b5b033cee8d 100644 (file)
--- a/src/tools/gmx_dipoles.c
+++ b/src/tools/gmx_dipoles.c
@@ -842,7 +842,7 @@ static void do_dip(t_topology *top, int ePBC, real volume,
         }
         if (iMu[XX] < 0 || iMu[YY] < 0 || iMu[ZZ] < 0)
         {
-            gmx_fatal(FARGS,"No index for Mu-X, Mu-Y or Mu-Z energy group.");
+            gmx_fatal(FARGS, "No index for Mu-X, Mu-Y or Mu-Z energy group.");
         }
     }
     else

diff --git a/src/tools/gmx_order.c b/src/tools/gmx_order.c
index b5f149a6c6ddc2dc22646d335246efa2f298ce22..fdc1ae2cb9b16960562b76a9921cde383ff5087d 100644 (file)
--- a/src/tools/gmx_order.c
+++ b/src/tools/gmx_order.c
@@ -402,8 +402,8 @@ void calc_order(const char *fn, atom_id *index, atom_id *a, rvec **order,
         size = 0,                                /* nr. of atoms in group. same as nr_tails        */
         i, j, m, k, l, teller = 0,
         slice,                                   /* current slice number                           */
-        nr_frames = 0,
-        *slCount;                                /* nr. of atoms in one slice                      */
+        nr_frames = 0;
+    int         *slCount;                        /* nr. of atoms in one slice                      */
     real         dbangle                = 0,     /* angle between double bond and  axis            */
                  sdbangle               = 0;     /* sum of these angles                            */
     gmx_bool     use_unitvector         = FALSE; /* use a specified unit vector instead of axis to specify unit normal*/
@@ -535,7 +535,7 @@ void calc_order(const char *fn, atom_id *index, atom_id *a, rvec **order,
             svmul(1.0/distsize, dref, dref);
             if (radial)
             {
-                pbc_dx(&pbc, dref, com, dvec);                
+                pbc_dx(&pbc, dref, com, dvec);
                 unitv(dvec, dvec);
             }
         }
@@ -667,22 +667,22 @@ void calc_order(const char *fn, atom_id *index, atom_id *a, rvec **order,
                     if (radial)
                     {
                         /* bin order parameter by arc distance from reference group*/
-                        arcdist = gmx_angle(dvec,direction);
+                        arcdist            = gmx_angle(dvec, direction);
                         (*distvals)[j][i] += arcdist;
                     }
                     else if (i == 1)
                     {
                         /* Want minimum lateral distance to first group calculated */
                         tmpdist = trace(box);  /* should be max value */
-                        for (k=0;k<distsize;k++)
+                        for (k = 0; k < distsize; k++)
                         {
                             pbc_dx(&pbc, x1[distidx[k]], x1[a[index[i]+j]], dvec);
                             /* at the moment, just remove dvec[axis] */
                             dvec[axis] = 0;
-                            tmpdist = min(tmpdist, norm2(dvec));
+                            tmpdist    = min(tmpdist, norm2(dvec));
                         }
-                    //fprintf(stderr, "Min dist %f; trace %f\n", tmpdist, trace(box));
-                    (*distvals)[j][i]+=sqrt(tmpdist);
+                        //fprintf(stderr, "Min dist %f; trace %f\n", tmpdist, trace(box));
+                        (*distvals)[j][i] += sqrt(tmpdist);
                     }
                 }
             } /* end loop j, over all atoms in group */

diff --git a/src/tools/gmx_tune_pme.c b/src/tools/gmx_tune_pme.c
index 4d4cd760020f7b8ab91dd565acb075f2800fc7a7..0563cffa6a824d01744ca2f4dd54a9a900ac02ff 100644 (file)
--- a/src/tools/gmx_tune_pme.c
+++ b/src/tools/gmx_tune_pme.c
@@ -1741,10 +1741,10 @@ static void check_input(
 /* Returns TRUE when "opt" is needed at launch time */
 static gmx_bool is_launch_file(char *opt, gmx_bool bSet)
 {
-    /* Apart from the input .tpr and the output log files we need all options that 
+    /* Apart from the input .tpr and the output log files we need all options that
      * were set on the command line and that do not start with -b */
-    if    (0 == strncmp(opt, "-b"  , 2) || 0 == strncmp(opt, "-s", 2) 
-        || 0 == strncmp(opt, "-err", 4) || 0 == strncmp(opt, "-p", 2) )
+    if    (0 == strncmp(opt, "-b", 2) || 0 == strncmp(opt, "-s", 2)
+           || 0 == strncmp(opt, "-err", 4) || 0 == strncmp(opt, "-p", 2) )
     {
         return FALSE;
     }